differential_count_models: rgedgeRpaired

annotate rgedgeRpaired_nocamera.xml @ 114:616c780f69a6 draft

Uploaded

author	fubar
date	Thu, 23 Oct 2014 00:05:56 -0400
parents	9f2e0ec3e826
children	badcd3b0e708

rev	line source
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	1 <tool id="rgDifferentialCount" name="Differential_Count" version="0.26">
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	2 <description>models using BioConductor packages</description>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	3 <requirements>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	4 <requirement type="package" version="2.14">biocbasics</requirement>
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	5 <requirement type="package" version="3.1.1">R_3_1_1</requirement>
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	6 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	7 <requirement type="package" version="9.10">ghostscript</requirement>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	8 </requirements>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	9
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	10 <command interpreter="python">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	11 rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	12 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	13 </command>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	14 <inputs>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	15 <param name="input1" type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	16 help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	17 <param name="title" type="text" value="Differential Counts" size="80" label="Title for job outputs"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	18 help="Supply a meaningful name here to remind you what the outputs contain">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	19 <sanitizer invalid_char="">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	20 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	21 </sanitizer>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	22 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	23 <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	24 <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	25 multiple="true" use_header_names="true" size="120" display="checkboxes">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	26 <validator type="no_options" message="Please select at least one column."/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	27 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	28 <param name="control_name" type="text" value="Control" size="50" label="Control Name"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	29 <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	30 multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	31 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	32 <param name="subjectids" type="text" optional="true" size="120" value = ""
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	33 label="IF SUBJECTS NOT ALL INDEPENDENT! Enter comma separated strings to indicate sample labels for (eg) pairing - must be one for every column in input"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	34 help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter 'A99,C21,A99,C21'">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	35 <sanitizer>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	36 <valid initial="string.letters,string.digits"><add value="," /> </valid>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	37 </sanitizer>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	38 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	39 <param name="fQ" type="float" value="0.3" size="5" label="Non-differential contig count quantile threshold - zero to analyze all non-zero read count contigs"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	40 help="May be a good or a bad idea depending on the biology and the question. EG 0.3 = sparsest 30% of contigs with at least one read are removed before analysis"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	41 <param name="useNDF" type="boolean" truevalue="T" falsevalue="F" checked="false" size="1"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	42 label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	43 help="May be a good or a bad idea depending on the biology and the question. This was the old default. Quantile based is available as an alternative"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	44
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	45 <conditional name="edgeR">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	46 <param name="doedgeR" type="select"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	47 label="Run this model using edgeR"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	48 help="edgeR uses a negative binomial model and seems to be powerful, even with few replicates">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	49 <option value="F">Do not run edgeR</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	50 <option value="T" selected="true">Run edgeR</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	51 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	52 <when value="T">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	53 <param name="edgeR_priordf" type="integer" value="10" size="3"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	54 label="prior.df for tagwise dispersion - larger value = more squeezing of tag dispersions to common dispersion. Replaces prior.n and prior.df = prior.n * residual.df"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	55 help="10 = edgeR default. Use a larger value to 'smooth' small samples. See edgeR docs and note below"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	56 <param name="edgeR_robust_method" type="select" value="20" size="3"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	57 label="Use robust dispersion method"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	58 help="Use ordinary, anscombe or deviance robust deviance estimates">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	59 <option value="ordinary" selected="true">Use ordinary deviance estimates</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	60 <option value="deviance">Use robust deviance estimates</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	61 <option value="anscombe">use Anscombe robust deviance estimates</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	62 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	63 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	64 <when value="F"></when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	65 </conditional>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	66 <conditional name="DESeq2">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	67 <param name="doDESeq2" type="select"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	68 label="Run the same model with DESeq2 and compare findings"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	69 help="DESeq2 is an update to the DESeq package. It uses different assumptions and methods to edgeR">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	70 <option value="F" selected="true">Do not run DESeq2</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	71 <option value="T">Run DESeq2</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	72 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	73 <when value="T">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	74 <param name="DESeq_fitType" type="select">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	75 <option value="parametric" selected="true">Parametric (default) fit for dispersions</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	76 <option value="local">Local fit - this will automagically be used if parametric fit fails</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	77 <option value="mean">Mean dispersion fit- use this if you really understand what you're doing - read the fine manual linked below in the documentation</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	78 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	79 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	80 <when value="F"> </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	81 </conditional>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	82 <param name="doVoom" type="select"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	83 label="Run the same model with Voom/limma and compare findings"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	84 help="Voom uses counts per million and a precise transformation of variance so count data can be analysed using limma">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	85 <option value="F" selected="true">Do not run VOOM</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	86 <option value="T">Run VOOM</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	87 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	88 <!--
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	89 <conditional name="camera">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	90 <param name="doCamera" type="select" label="Run the edgeR implementation of Camera GSEA for up/down gene sets"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	91 help="If yes, you can choose a set of genesets to test and/or supply a gmt format geneset collection from your history">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	92 <option value="F" selected="true">Do not run GSEA tests with the Camera algorithm</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	93 <option value="T">Run GSEA tests with the Camera algorithm</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	94 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	95 <when value="T">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	96 <conditional name="gmtSource">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	97 <param name="refgmtSource" type="select"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	98 label="Use a gene set (.gmt) from your history and/or use a built-in (MSigDB etc) gene set">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	99 <option value="indexed" selected="true">Use a built-in gene set</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	100 <option value="history">Use a gene set from my history</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	101 <option value="both">Add a gene set from my history to a built in gene set</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	102 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	103 <when value="indexed">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	104 <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	105 <options from_data_table="gseaGMT_3.1">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	106 <filter type="sort_by" column="2" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	107 <validator type="no_options" message="No GMT v3.1 files are available - please install them"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	108 </options>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	109 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	110 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	111 <when value="history">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	112 <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	113 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	114 <when value="both">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	115 <param name="ownGMT" type="data" format="gseagmt" label="Select a Gene Set from your history" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	116 <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	117 <options from_data_table="gseaGMT_4">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	118 <filter type="sort_by" column="2" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	119 <validator type="no_options" message="No GMT v4 files are available - please fix tool_data_table and loc files"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	120 </options>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	121 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	122 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	123 </conditional>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	124 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	125 <when value="F">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	126 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	127 </conditional>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	128 -->
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	129 <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	130 help="Conventional default value of 0.05 recommended"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	131 <param name="fdrtype" type="select" label="FDR (Type II error) control method"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	132 help="Use fdr or bh typically to control for the number of tests in a reliable way">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	133 <option value="fdr" selected="true">fdr</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	134 <option value="BH">Benjamini Hochberg</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	135 <option value="BY">Benjamini Yukateli</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	136 <option value="bonferroni">Bonferroni</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	137 <option value="hochberg">Hochberg</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	138 <option value="holm">Holm</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	139 <option value="hommel">Hommel</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	140 <option value="none">no control for multiple tests</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	141 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	142 </inputs>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	143 <outputs>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	144 <data format="tabular" name="out_edgeR" label="${title}_topTable_edgeR.xls">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	145 <filter>edgeR['doedgeR'] == "T"</filter>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	146 </data>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	147 <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	148 <filter>DESeq2['doDESeq2'] == "T"</filter>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	149 </data>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	150 <data format="tabular" name="out_VOOM" label="${title}_topTable_VOOM.xls">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	151 <filter>doVoom == "T"</filter>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	152 </data>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	153 <data format="html" name="html_file" label="${title}.html"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	154 </outputs>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	155 <stdio>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	156 <exit_code range="4" level="fatal" description="Number of subject ids must match total number of samples in the input matrix" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	157 </stdio>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	158 <tests>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	159 <test>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	160 <param name='input1' value='test_bams2mx.xls' ftype='tabular' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	161 <param name='treatment_name' value='liver' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	162 <param name='title' value='edgeRtest' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	163 <param name='useNDF' value='' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	164 <param name='doedgeR' value='T' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	165 <param name='doVoom' value='T' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	166 <param name='doDESeq2' value='T' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	167 <param name='fdrtype' value='fdr' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	168 <param name='edgeR_priordf' value="8" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	169 <param name='edgeR_robust' value="ordinary" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	170 <param name='fdrthresh' value="0.05" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	171 <param name='control_name' value='heart' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	172 <param name='subjectids' value='' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	173 <param name='Control_cols' value='3,4,5,9' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	174 <param name='Treat_cols' value='2,6,7,8' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	175 <output name='out_edgeR' file='edgeRtest1out.xls' compare='diff' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	176 <output name='html_file' file='edgeRtest1out.html' compare='diff' lines_diff='20' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	177 </test>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	178 </tests>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	179
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	180 <configfiles>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	181 <configfile name="runme">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	182 <![CDATA[
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	183 #
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	184 # edgeR.Rscript
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	185 # updated feb 2014 adding outlier-robust deviance estimate options by ross for R 3.0.2/bioc 2.13
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	186 # updated npv 2011 for R 2.14.0 and edgeR 2.4.0 by ross
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	187 # Performs DGE on a count table containing n replicates of two conditions
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	188 #
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	189 # Parameters
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	190 #
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	191 # 1 - Output Dir
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	192
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	193 # Original edgeR code by: S.Lunke and A.Kaspi
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	194 reallybig = log10(.Machine\$double.xmax)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	195 reallysmall = log10(.Machine\$double.xmin)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	196 library("stringr")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	197 library("gplots")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	198 library("edgeR")
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	199 hmap2 = function(cmat,nsamp=100,outpdfname='heatmap2.pdf', TName='Treatment',group=NA,myTitle='title goes here')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	200 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	201 # Perform clustering for significant pvalues after controlling FWER
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	202 samples = colnames(cmat)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	203 gu = unique(group)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	204 gn = rownames(cmat)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	205 if (length(gu) == 2) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	206 col.map = function(g) {if (g==gu[1]) "#FF0000" else "#0000FF"}
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	207 pcols = unlist(lapply(group,col.map))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	208 } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	209 colours = rainbow(length(gu),start=0,end=4/6)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	210 pcols = colours[match(group,gu)] }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	211 dm = cmat[(! is.na(gn)),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	212 # remove unlabelled hm rows
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	213 nprobes = nrow(dm)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	214 # sub = paste('Showing',nprobes,'contigs ranked for evidence of differential abundance')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	215 if (nprobes > nsamp) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	216 dm =dm[1:nsamp,]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	217 #sub = paste('Showing',nsamp,'contigs ranked for evidence for differential abundance out of',nprobes,'total')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	218 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	219 newcolnames = substr(colnames(dm),1,20)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	220 colnames(dm) = newcolnames
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	221 pdf(outpdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	222 heatmap.2(dm,main=myTitle,ColSideColors=pcols,col=topo.colors(100),dendrogram="col",key=T,density.info='none',
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	223 Rowv=F,scale='row',trace='none',margins=c(8,8),cexRow=0.4,cexCol=0.5)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	224 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	225 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	226
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	227 hmap = function(cmat,nmeans=4,outpdfname="heatMap.pdf",nsamp=250,TName='Treatment',group=NA,myTitle="Title goes here")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	228 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	229 # for 2 groups only was
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	230 #col.map = function(g) {if (g==TName) "#FF0000" else "#0000FF"}
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	231 #pcols = unlist(lapply(group,col.map))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	232 gu = unique(group)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	233 colours = rainbow(length(gu),start=0.3,end=0.6)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	234 pcols = colours[match(group,gu)]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	235 nrows = nrow(cmat)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	236 mtitle = paste(myTitle,'Heatmap: n contigs =',nrows)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	237 if (nrows > nsamp) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	238 cmat = cmat[c(1:nsamp),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	239 mtitle = paste('Heatmap: Top ',nsamp,' DE contigs (of ',nrows,')',sep='')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	240 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	241 newcolnames = substr(colnames(cmat),1,20)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	242 colnames(cmat) = newcolnames
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	243 pdf(outpdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	244 heatmap(cmat,scale='row',main=mtitle,cexRow=0.3,cexCol=0.4,Rowv=NA,ColSideColors=pcols)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	245 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	246 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	247
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	248 qqPlot = function(descr='qqplot',pvector, outpdf='qqplot.pdf',...)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	249 # stolen from https://gist.github.com/703512
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	250 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	251 o = -log10(sort(pvector,decreasing=F))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	252 e = -log10( 1:length(o)/length(o) )
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	253 o[o==-Inf] = reallysmall
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	254 o[o==Inf] = reallybig
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	255 maint = descr
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	256 pdf(outpdf)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	257 plot(e,o,pch=19,cex=1, main=maint, ...,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	258 xlab=expression(Expected~~-log[10](italic(p))),
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	259 ylab=expression(Observed~~-log[10](italic(p))),
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	260 xlim=c(0,max(e)), ylim=c(0,max(o)))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	261 lines(e,e,col="red")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	262 grid(col = "lightgray", lty = "dotted")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	263 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	264 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	265
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	266 smearPlot = function(myDGEList,deTags, outSmear, outMain)
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	267 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	268 pdf(outSmear)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	269 plotSmear(myDGEList,de.tags=deTags,main=outMain)
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	270 grid(col="lightgray", lty="dotted")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	271 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	272 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	273
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	274 boxPlot = function(rawrs,cleanrs,maint,myTitle,pdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	275 { #
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	276 nc = ncol(rawrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	277 for (i in c(1:nc)) {rawrs[(rawrs[,i] < 0),i] = NA}
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	278 fullnames = colnames(rawrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	279 newcolnames = substr(colnames(rawrs),1,20)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	280 colnames(rawrs) = newcolnames
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	281 newcolnames = substr(colnames(cleanrs),1,20)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	282 colnames(cleanrs) = newcolnames
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	283 defpar = par(no.readonly=T)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	284 print.noquote('raw contig counts by sample:')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	285 print.noquote(summary(rawrs))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	286 print.noquote('normalised contig counts by sample:')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	287 print.noquote(summary(cleanrs))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	288 pdf(pdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	289 par(mfrow=c(1,2))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	290 boxplot(rawrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('Raw:',maint))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	291 grid(col="lightgray",lty="dotted")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	292 boxplot(cleanrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('After ',maint))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	293 grid(col="lightgray",lty="dotted")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	294 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	295 pdfname = "sample_counts_histogram.pdf"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	296 nc = ncol(rawrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	297 print.noquote(paste('Using ncol rawrs=',nc))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	298 ncroot = round(sqrt(nc))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	299 if (ncroot*ncroot < nc) { ncroot = ncroot + 1 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	300 m = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	301 for (i in c(1:nc)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	302 rhist = hist(rawrs[,i],breaks=100,plot=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	303 m = append(m,max(rhist\$counts))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	304 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	305 ymax = max(m)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	306 ncols = length(fullnames)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	307 if (ncols > 20)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	308 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	309 scale = 7*ncols/20
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	310 pdf(pdfname,width=scale,height=scale)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	311 } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	312 pdf(pdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	313 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	314 par(mfrow=c(ncroot,ncroot))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	315 for (i in c(1:nc)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	316 hist(rawrs[,i], main=paste("Contig logcount",i), xlab='log raw count', col="maroon",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	317 breaks=100,sub=fullnames[i],cex=0.8,ylim=c(0,ymax))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	318 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	319 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	320 par(defpar)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	321
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	322 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	323
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	324 cumPlot = function(rawrs,cleanrs,maint,myTitle)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	325 { # updated to use ecdf
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	326 pdfname = "Filtering_rowsum_bar_charts.pdf"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	327 defpar = par(no.readonly=T)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	328 lrs = log(rawrs,10)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	329 lim = max(lrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	330 pdf(pdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	331 par(mfrow=c(2,1))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	332 hist(lrs,breaks=100,main=paste('Before:',maint),xlab="# Reads (log)",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	333 ylab="Count",col="maroon",sub=myTitle, xlim=c(0,lim),las=1)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	334 grid(col="lightgray", lty="dotted")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	335 lrs = log(cleanrs,10)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	336 hist(lrs,breaks=100,main=paste('After:',maint),xlab="# Reads (log)",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	337 ylab="Count",col="maroon",sub=myTitle,xlim=c(0,lim),las=1)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	338 grid(col="lightgray", lty="dotted")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	339 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	340 par(defpar)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	341 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	342
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	343 cumPlot1 = function(rawrs,cleanrs,maint,myTitle)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	344 { # updated to use ecdf
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	345 pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"RowsumCum.pdf",sep='_')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	346 pdf(pdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	347 par(mfrow=c(2,1))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	348 lastx = max(rawrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	349 rawe = knots(ecdf(rawrs))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	350 cleane = knots(ecdf(cleanrs))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	351 cy = 1:length(cleane)/length(cleane)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	352 ry = 1:length(rawe)/length(rawe)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	353 plot(rawe,ry,type='l',main=paste('Before',maint),xlab="Log Contig Total Reads",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	354 ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	355 grid(col="blue")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	356 plot(cleane,cy,type='l',main=paste('After',maint),xlab="Log Contig Total Reads",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	357 ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	358 grid(col="blue")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	359 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	360 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	361
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	362
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	363
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	364 doGSEAold = function(y=NULL,design=NULL,histgmt="",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	365 bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	366 ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	367 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	368 sink('Camera.log')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	369 genesets = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	370 if (bigmt > "")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	371 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	372 bigenesets = readLines(bigmt)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	373 genesets = bigenesets
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	374 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	375 if (histgmt > "")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	376 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	377 hgenesets = readLines(histgmt)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	378 if (bigmt > "") {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	379 genesets = rbind(genesets,hgenesets)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	380 } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	381 genesets = hgenesets
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	382 } # use only history if no bi
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	383 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	384 print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	385 genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	386 outf = outfname
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	387 head=paste(myTitle,'edgeR GSEA')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	388 write(head,file=outfname,append=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	389 ntest=length(genesets)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	390 urownames = toupper(rownames(y))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	391 upcam = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	392 downcam = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	393 for (i in 1:ntest) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	394 gs = unlist(genesets[i])
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	395 g = gs[1] # geneset_id
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	396 u = gs[2]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	397 if (u > "") { u = paste("<a href=\'",u,"\'>",u,"</a>",sep="") }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	398 glist = gs[3:length(gs)] # member gene symbols
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	399 glist = toupper(glist)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	400 inglist = urownames %in% glist
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	401 nin = sum(inglist)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	402 if ((nin > minnin) && (nin < maxnin)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	403 ### print(paste('@@found',sum(inglist),'genes in glist'))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	404 camres = camera(y=y,index=inglist,design=design)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	405 if (! is.null(camres)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	406 rownames(camres) = g # gene set name
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	407 camres = cbind(GeneSet=g,URL=u,camres)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	408 if (camres\$Direction == "Up")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	409 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	410 upcam = rbind(upcam,camres) } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	411 downcam = rbind(downcam,camres)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	412 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	413 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	414 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	415 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	416 uscam = upcam[order(upcam\$PValue),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	417 unadjp = uscam\$PValue
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	418 uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	419 nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	420 dscam = downcam[order(downcam\$PValue),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	421 unadjp = dscam\$PValue
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	422 dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	423 ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	424 write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	425 write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	426 print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	427 write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	428 print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	429 write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	430 sink()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	431 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	432
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	433
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	434
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	435
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	436 doGSEA = function(y=NULL,design=NULL,histgmt="",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	437 bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	438 ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	439 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	440 sink('Camera.log')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	441 genesets = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	442 if (bigmt > "")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	443 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	444 bigenesets = readLines(bigmt)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	445 genesets = bigenesets
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	446 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	447 if (histgmt > "")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	448 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	449 hgenesets = readLines(histgmt)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	450 if (bigmt > "") {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	451 genesets = rbind(genesets,hgenesets)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	452 } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	453 genesets = hgenesets
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	454 } # use only history if no bi
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	455 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	456 print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	457 genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	458 outf = outfname
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	459 head=paste(myTitle,'edgeR GSEA')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	460 write(head,file=outfname,append=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	461 ntest=length(genesets)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	462 urownames = toupper(rownames(y))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	463 upcam = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	464 downcam = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	465 incam = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	466 urls = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	467 gsids = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	468 for (i in 1:ntest) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	469 gs = unlist(genesets[i])
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	470 gsid = gs[1] # geneset_id
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	471 url = gs[2]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	472 if (url > "") { url = paste("<a href=\'",url,"\'>",url,"</a>",sep="") }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	473 glist = gs[3:length(gs)] # member gene symbols
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	474 glist = toupper(glist)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	475 inglist = urownames %in% glist
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	476 nin = sum(inglist)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	477 if ((nin > minnin) && (nin < maxnin)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	478 incam = c(incam,inglist)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	479 gsids = c(gsids,gsid)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	480 urls = c(urls,url)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	481 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	482 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	483 incam = as.list(incam)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	484 names(incam) = gsids
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	485 allcam = camera(y=y,index=incam,design=design)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	486 allcamres = cbind(geneset=gsids,allcam,URL=urls)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	487 for (i in 1:ntest) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	488 camres = allcamres[i]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	489 res = try(test = (camres\$Direction == "Up"))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	490 if ("try-error" %in% class(res)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	491 cat("test failed, camres = :")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	492 print.noquote(camres)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	493 } else { if (camres\$Direction == "Up")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	494 { upcam = rbind(upcam,camres)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	495 } else { downcam = rbind(downcam,camres)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	496 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	497
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	498 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	499 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	500 uscam = upcam[order(upcam\$PValue),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	501 unadjp = uscam\$PValue
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	502 uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	503 nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	504 dscam = downcam[order(downcam\$PValue),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	505 unadjp = dscam\$PValue
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	506 dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	507 ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	508 write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	509 write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	510 print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	511 write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	512 print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	513 write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	514 sink()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	515 }
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	516
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	517
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	518 edgeIt = function (Count_Matrix=c(),group=c(),out_edgeR=F,out_Voom=F,out_DESeq2=F,fdrtype='fdr',priordf=5,
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	519 fdrthresh=0.05,outputdir='.', myTitle='Differential Counts',libSize=c(),useNDF=F,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	520 filterquantile=0.2, subjects=c(),mydesign=NULL,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	521 doDESeq2=T,doVoom=T,doCamera=T,doedgeR=T,org='hg19',
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	522 histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	523 doCook=F,DESeq_fitType="parameteric",robust_meth='ordinary')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	524 {
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	525
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	526
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	527 run_edgeR = function(workCM,pdata,subjects,group,priordf,robust_meth,mydesign,mt,cmrowsums,out_edgeR)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	528 {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	529 sink('edgeR.log')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	530 #### Setup myDGEList object
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	531 myDGEList = DGEList(counts=workCM, group = group)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	532 myDGEList = calcNormFactors(myDGEList)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	533 if (robust_meth == 'ordinary') {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	534 myDGEList = estimateGLMCommonDisp(myDGEList,mydesign)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	535 myDGEList = estimateGLMTrendedDisp(myDGEList,mydesign)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	536 if (priordf > 0) { myDGEList = estimateGLMTagwiseDisp(myDGEList,mydesign,prior.df = priordf)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	537 } else { myDGEList = estimateGLMTagwiseDisp(myDGEList,mydesign) }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	538 comdisp = myDGEList\$common.dispersion
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	539 estpriorn = getPriorN(myDGEList)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	540 print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	541 } else {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	542 myDGEList = estimateGLMRobustDisp(myDGEList,design=mydesign, prior.df = priordf, maxit = 6, residual.type = robust_meth)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	543 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	544
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	545
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	546 DGLM = glmFit(myDGEList,design=mydesign)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	547 DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	548 efflib = myDGEList\$samples\$lib.size*myDGEList\$samples\$norm.factors
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	549 normData = (1e+06*myDGEList\$counts/efflib)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	550 uoutput = cbind(
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	551 Name=as.character(rownames(myDGEList\$counts)),
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	552 DE\$table,
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	553 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	554 Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums,normData,
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	555 myDGEList\$counts
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	556 )
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	557 soutput = uoutput[order(DE\$table\$PValue),] # sorted into p value order - for quick toptable
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	558 goodness = gof(DGLM, pcutoff=fdrthresh)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	559 if (sum(goodness\$outlier) > 0) {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	560 print.noquote('GLM outliers:')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	561 print(paste(rownames(DGLM)[(goodness\$outlier)],collapse=','),quote=F)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	562 } else {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	563 print('No GLM fit outlier genes found\n')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	564 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	565 z = limma::zscoreGamma(goodness\$gof.statistic, shape=goodness\$df/2, scale=2)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	566 pdf(paste("edgeR",mt,"GoodnessofFit.pdf",sep='_'))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	567 qq = qqnorm(z, panel.first=grid(), main="tagwise dispersion")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	568 abline(0,1,lwd=3)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	569 points(qq\$x[goodness\$outlier],qq\$y[goodness\$outlier], pch=16, col="maroon")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	570 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	571 uniqueg = unique(group)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	572 #### Plot MDS
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	573 sample_colors = match(group,levels(group))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	574 sampleTypes = levels(factor(group))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	575 print.noquote(sampleTypes)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	576 pdf(paste("edgeR",mt,"MDSplot.pdf",sep='_'))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	577 plotMDS.DGEList(myDGEList,main=paste("edgeR MDS for",myTitle),cex=0.5,col=sample_colors,pch=sample_colors)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	578 legend(x="topleft", legend = sampleTypes,col=c(1:length(sampleTypes)), pch=19)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	579 grid(col="blue")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	580 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	581 colnames(normData) = paste( colnames(normData),'N',sep="_")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	582 print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=',')))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	583 nzd = data.frame(log(nonzerod + 1e-2,10))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	584 try( boxPlot(rawrs=nzd,cleanrs=log(normData,10),maint='TMM Normalisation',myTitle=myTitle,pdfname=paste("edgeR",mt,"raw_norm_counts_box.pdf",sep='_') ))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	585 write.table(soutput,file=out_edgeR, quote=FALSE, sep="\t",row.names=F)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	586 tt = cbind(
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	587 Name=as.character(rownames(myDGEList)),
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	588 DE\$table,
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	589 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	590 Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	591 )
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	592 print.noquote("# edgeR Top tags\n")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	593 tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	594 tt = tt[order(DE\$table\$PValue),]
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	595 print.noquote(tt[1:50,])
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	596 deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,])
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	597 nsig = length(deTags)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	598 print(paste('#',nsig,'tags significant at adj p=',fdrthresh),quote=F)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	599 deColours = ifelse(deTags,'red','black')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	600 pdf(paste("edgeR",mt,"BCV_vs_abundance.pdf",sep="_"))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	601 plotBCV(myDGEList, cex=0.3, main="Biological CV vs abundance")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	602 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	603 dg = myDGEList[order(DE\$table\$PValue),]
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	604 #normData = (1e+06 * dg\$counts/expandAsMatrix(dg\$samples\$lib.size, dim(dg)))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	605 outpdfname= paste("edgeR",mt,"top_100_heatmap.pdf",sep="_")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	606 hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste(myTitle,'Heatmap'))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	607 outSmear = paste("edgeR",mt,"smearplot.pdf",sep="_")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	608 outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	609 smearPlot(myDGEList=myDGEList,deTags=deTags, outSmear=outSmear, outMain = outMain)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	610 qqPlot(descr=paste(myTitle,'edgeR adj p QQ plot'),pvector=tt\$adj.p.value,outpdf=paste('edgeR',mt,'qqplot.pdf',sep='_'))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	611 norm.factor = myDGEList\$samples\$norm.factors
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	612 topresults.edgeR = soutput[which(soutput\$adj.p.value < fdrthresh), ]
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	613 edgeRcountsindex = which(allgenes %in% rownames(topresults.edgeR))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	614 edgeRcounts = rep(0, length(allgenes))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	615 edgeRcounts[edgeRcountsindex] = 1 # Create venn diagram of hits
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	616 sink()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	617 return(list(myDGEList=myDGEList,edgeRcounts=edgeRcounts))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	618 } ### run_edgeR
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	619
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	620
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	621 run_DESeq2 = function(workCM,pdata,subjects,group,out_DESeq2,mt,DESeq_fitType)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	622
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	623 {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	624 sink("DESeq2.log")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	625 # DESeq2
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	626 require('DESeq2')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	627 library('RColorBrewer')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	628 if (length(subjects) == 0)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	629 {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	630 pdata = data.frame(Name=colnames(workCM),Rx=group,row.names=colnames(workCM))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	631 deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ Rx))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	632 } else {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	633 pdata = data.frame(Name=colnames(workCM),Rx=group,subjects=subjects,row.names=colnames(workCM))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	634 deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ subjects + Rx))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	635 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	636 #DESeq2 = DESeq(deSEQds,fitType='local',pAdjustMethod=fdrtype)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	637 #rDESeq = results(DESeq2)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	638 #newCountDataSet(workCM, group)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	639 deSeqDatsizefac = estimateSizeFactors(deSEQds)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	640 deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	641 resDESeq = nbinomWaldTest(deSeqDatdisp)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	642 rDESeq = as.data.frame(results(resDESeq))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	643 rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums,URL=contigurls)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	644 srDESeq = rDESeq[order(rDESeq\$pvalue),]
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	645 qqPlot(descr=paste(myTitle,'DESeq2 adj p qq plot'),pvector=rDESeq\$padj,outpdf=paste('DESeq2',mt,'qqplot.pdf',sep="_"))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	646 cat("# DESeq top 50\n")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	647 print.noquote(srDESeq[1:50,])
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	648 write.table(srDESeq,file=out_DESeq2, quote=FALSE, sep="\t",row.names=F)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	649 topresults.DESeq = rDESeq[which(rDESeq\$padj < fdrthresh), ]
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	650 DESeqcountsindex = which(allgenes %in% rownames(topresults.DESeq))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	651 DESeqcounts = rep(0, length(allgenes))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	652 DESeqcounts[DESeqcountsindex] = 1
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	653 pdf(paste("DESeq2",mt,"dispersion_estimates.pdf",sep='_'))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	654 plotDispEsts(resDESeq)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	655 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	656 ysmall = abs(min(rDESeq\$log2FoldChange))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	657 ybig = abs(max(rDESeq\$log2FoldChange))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	658 ylimit = min(4,ysmall,ybig)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	659 pdf(paste("DESeq2",mt,"MA_plot.pdf",sep="_"))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	660 plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	661 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	662 rlogres = rlogTransformation(resDESeq)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	663 sampledists = dist( t( assay(rlogres) ) )
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	664 sdmat = as.matrix(sampledists)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	665 pdf(paste("DESeq2",mt,"sample_distance_plot.pdf",sep="_"))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	666 heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"),
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	667 col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	668 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	669 ###outpdfname=paste("DESeq2",mt,"top50_heatmap.pdf",sep="_")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	670 ###hmap2(sresDESeq,nsamp=50,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('DESeq2 vst rlog Heatmap',myTitle))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	671 sink()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	672 result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) )
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	673 if ("try-error" %in% class(result)) {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	674 print.noquote('DESeq2 plotPCA failed.')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	675 } else {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	676 pdf(paste("DESeq2",mt,"PCA_plot.pdf",sep="_"))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	677 #### wtf - print? Seems needed to get this to work
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	678 print(ppca)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	679 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	680 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	681 return(DESeqcounts)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	682 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	683
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	684
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	685 run_Voom = function(workCM,pdata,subjects,group,mydesign,mt,out_Voom)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	686 {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	687 sink('VOOM.log')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	688 if (doedgeR == F) {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	689 #### Setup myDGEList object
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	690 myDGEList = DGEList(counts=workCM, group = group)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	691 myDGEList = calcNormFactors(myDGEList)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	692 myDGEList = estimateGLMCommonDisp(myDGEList,mydesign)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	693 myDGEList = estimateGLMTrendedDisp(myDGEList,mydesign)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	694 myDGEList = estimateGLMTagwiseDisp(myDGEList,mydesign)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	695 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	696 pdf(paste("VOOM",mt,"mean_variance_plot.pdf",sep='_'))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	697 dat.voomed <- voom(myDGEList, mydesign, plot = TRUE, normalize.method="quantil", lib.size = NULL)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	698 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	699 # Use limma to fit data
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	700 fit = lmFit(dat.voomed, mydesign)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	701 fit = eBayes(fit)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	702 rvoom = topTable(fit, coef = length(colnames(mydesign)), adj = fdrtype, n = Inf, sort="none")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	703 qqPlot(descr=paste(myTitle,'VOOM-limma adj p QQ plot'),pvector=rvoom\$adj.P.Val,outpdf=paste('VOOM',mt,'qqplot.pdf',sep='_'))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	704 rownames(rvoom) = rownames(workCM)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	705 rvoom = cbind(rvoom,NReads=cmrowsums,URL=contigurls)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	706 srvoom = rvoom[order(rvoom\$P.Value),]
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	707 cat("# VOOM top 50\n")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	708 print(srvoom[1:50,])
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	709 write.table(srvoom,file=out_Voom, quote=FALSE, sep="\t",row.names=F)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	710 # Use an FDR cutoff to find interesting samples for edgeR, DESeq and voom/limma
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	711 topresults.voom = rvoom[which(rvoom\$adj.P.Val < fdrthresh), ]
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	712 voomcountsindex <- which(allgenes %in% rownames(topresults.voom))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	713 voomcounts = rep(0, length(allgenes))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	714 voomcounts[voomcountsindex] = 1
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	715 sink()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	716 return(voomcounts)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	717 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	718
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	719
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	720 #### data cleaning and analsis control starts here
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	721
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	722 # Error handling
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	723 nugroup = length(unique(group))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	724 if (nugroup!=2){
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	725 print("Number of conditions identified in experiment does not equal 2")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	726 q()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	727 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	728 require(edgeR)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	729 options(width = 512)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	730 mt = paste(unlist(strsplit(myTitle,'_')),collapse=" ")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	731 allN = nrow(Count_Matrix)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	732 nscut = round(ncol(Count_Matrix)/2) # half samples
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	733 colTotmillionreads = colSums(Count_Matrix)/1e6
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	734 counts.dataframe = as.data.frame(c())
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	735 rawrs = rowSums(Count_Matrix)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	736 nonzerod = Count_Matrix[(rawrs > 0),] # remove all zero count genes
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	737 nzN = nrow(nonzerod)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	738 nzrs = rowSums(nonzerod)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	739 zN = allN - nzN
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	740 print('# Quantiles for non-zero row counts:',quote=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	741 print(quantile(nzrs,probs=seq(0,1,0.1)),quote=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	742 if (useNDF == T)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	743 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	744 gt1rpin3 = rowSums(Count_Matrix/expandAsMatrix(colTotmillionreads,dim(Count_Matrix)) >= 1) >= nscut
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	745 lo = colSums(Count_Matrix[!gt1rpin3,])
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	746 workCM = Count_Matrix[gt1rpin3,]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	747 cleanrs = rowSums(workCM)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	748 cleanN = length(cleanrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	749 meth = paste( "After removing",length(lo),"contigs with fewer than ",nscut," sample read counts >= 1 per million, there are",sep="")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	750 print(paste("Read",allN,"contigs. Removed",zN,"contigs with no reads.",meth,cleanN,"contigs"),quote=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	751 maint = paste('Filter >=1/million reads in >=',nscut,'samples')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	752 } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	753 useme = (nzrs > quantile(nzrs,filterquantile))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	754 workCM = nonzerod[useme,]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	755 lo = colSums(nonzerod[!useme,])
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	756 cleanrs = rowSums(workCM)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	757 cleanN = length(cleanrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	758 meth = paste("After filtering at count quantile =",filterquantile,", there are",sep="")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	759 print(paste('Read',allN,"contigs. Removed",zN,"with no reads.",meth,cleanN,"contigs"),quote=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	760 maint = paste('Filter below',filterquantile,'quantile')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	761 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	762 cumPlot(rawrs=rawrs,cleanrs=cleanrs,maint=maint,myTitle=myTitle)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	763 allgenes = rownames(workCM)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	764 reg = "^chr([0-9]+):([0-9]+)-([0-9]+)" # ucsc chr:start-end regexp
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	765 genecards="<a href=\'http://www.genecards.org/index.php?path=/Search/keyword/"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	766 ucsc = paste("<a href=\'http://genome.ucsc.edu/cgi-bin/hgTracks?db=",org,sep='')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	767 testreg = str_match(allgenes,reg)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	768 if (sum(!is.na(testreg[,1]))/length(testreg[,1]) > 0.8) # is ucsc style string
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	769 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	770 print("@@ using ucsc substitution for urls")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	771 contigurls = paste0(ucsc,"&position=chr",testreg[,2],":",testreg[,3],"-",testreg[,4],"\'>",allgenes,"</a>")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	772 } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	773 print("@@ using genecards substitution for urls")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	774 contigurls = paste0(genecards,allgenes,"\'>",allgenes,"</a>")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	775 }
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	776 print.noquote("# urls sample")
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	777 print.noquote(head(contigurls))
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	778 print(paste("# Total low count contigs per sample = ",table(lo)),quote=F)
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	779 cmrowsums = rowSums(workCM)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	780 TName=unique(group)[1]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	781 CName=unique(group)[2]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	782 if (is.null(mydesign)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	783 if (length(subjects) == 0)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	784 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	785 mydesign = model.matrix(~group)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	786 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	787 else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	788 subjf = factor(subjects)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	789 mydesign = model.matrix(~subjf+group) # we block on subject so make group last to simplify finding it
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	790 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	791 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	792 print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=',')))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	793 print.noquote('Using design matrix:')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	794 print.noquote(mydesign)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	795 if (doedgeR == T) {
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	796 eres = run_edgeR(workCM,pdata,subjects,group,priordf,robust_meth,mydesign,mt,cmrowsums,out_edgeR)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	797 myDGEList = eres\$myDGEList
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	798 edgeRcounts = eres\$edgeRcounts
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	799 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	800 if (doDESeq2 == T) { DESeqcounts = run_DESeq2(workCM,pdata,subjects,group,out_DESeq2,mt,DESeq_fitType) }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	801 if (doVoom == T) { voomcounts = run_Voom(workCM,pdata,subjects,group,mydesign,mt,out_Voom) }
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	802
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	803
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	804 if (doCamera) {
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	805 doGSEA(y=myDGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle,
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	806 outfname=paste("GSEA_Camera",mt,"table.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype)
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	807 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	808 counts.dataframe = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	809 vennmain = 'no venn'
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	810 if ((doDESeq2==T) \|\| (doVoom==T) \|\| (doedgeR==T)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	811 if ((doVoom==T) && (doDESeq2==T) && (doedgeR==T)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	812 vennmain = paste(mt,'Voom,edgeR and DESeq2 overlap at FDR=',fdrthresh)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	813 counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	814 VOOM_limma = voomcounts, row.names = allgenes)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	815 } else if ((doDESeq2==T) && (doedgeR==T)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	816 vennmain = paste(mt,'DESeq2 and edgeR overlap at FDR=',fdrthresh)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	817 counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, row.names = allgenes)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	818 } else if ((doVoom==T) && (doedgeR==T)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	819 vennmain = paste(mt,'Voom and edgeR overlap at FDR=',fdrthresh)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	820 counts.dataframe = data.frame(edgeR = edgeRcounts, VOOM_limma = voomcounts, row.names = allgenes)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	821 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	822
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	823 if (nrow(counts.dataframe > 1)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	824 counts.venn = vennCounts(counts.dataframe)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	825 vennf = paste("Venn",mt,"significant_genes_overlap.pdf",sep="_")
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	826 pdf(vennf)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	827 vennDiagram(counts.venn,main=vennmain,col="maroon")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	828 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	829 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	830 } #### doDESeq2 or doVoom
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	831
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	832 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	833 #### Done
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	834
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	835 ###sink(stdout(),append=T,type="message")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	836 builtin_gmt = ""
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	837 history_gmt = ""
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	838 history_gmt_name = ""
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	839 out_edgeR = F
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	840 out_DESeq2 = F
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	841 out_Voom = "$out_VOOM"
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	842 edgeR_robust_meth = "ordinary" # control robust deviance options
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	843 doDESeq2 = $DESeq2.doDESeq2
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	844 doVoom = $doVoom
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	845 doCamera = F
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	846 doedgeR = $edgeR.doedgeR
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	847 edgeR_priordf = 10
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	848
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	849
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	850 #if $doVoom == "T":
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	851 out_Voom = "$out_VOOM"
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	852 #end if
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	853
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	854 #if $DESeq2.doDESeq2 == "T":
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	855 out_DESeq2 = "$out_DESeq2"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	856 doDESeq2 = T
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	857 DESeq_fitType = "$DESeq2.DESeq_fitType"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	858 #end if
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	859
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	860 #if $edgeR.doedgeR == "T":
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	861 out_edgeR = "$out_edgeR"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	862 edgeR_priordf = $edgeR.edgeR_priordf
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	863 edgeR_robust_meth = "$edgeR.edgeR_robust_method"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	864 #end if
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	865
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	866
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	867 if (sum(c(doedgeR,doVoom,doDESeq2)) == 0)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	868 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	869 write("No methods chosen - nothing to do! Please try again after choosing one or more methods", stderr())
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	870 quit(save="no",status=2)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	871 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	872
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	873 Out_Dir = "$html_file.files_path"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	874 Input = "$input1"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	875 TreatmentName = "$treatment_name"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	876 TreatmentCols = "$Treat_cols"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	877 ControlName = "$control_name"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	878 ControlCols= "$Control_cols"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	879 org = "$input1.dbkey"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	880 if (org == "") { org = "hg19"}
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	881 fdrtype = "$fdrtype"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	882 fdrthresh = $fdrthresh
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	883 useNDF = $useNDF
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	884 fQ = $fQ # non-differential centile cutoff
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	885 myTitle = "$title"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	886 sids = strsplit("$subjectids",',')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	887 subjects = unlist(sids)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	888 nsubj = length(subjects)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	889 TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	890 CCols = as.numeric(strsplit(ControlCols,",")[[1]])-1
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	891 cat('Got TCols=')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	892 cat(TCols)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	893 cat('; CCols=')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	894 cat(CCols)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	895 cat('\n')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	896 useCols = c(TCols,CCols)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	897 if (file.exists(Out_Dir) == F) dir.create(Out_Dir)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	898 Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t') #Load tab file assume header
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	899 snames = colnames(Count_Matrix)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	900 nsamples = length(snames)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	901 if (nsubj > 0 & nsubj != nsamples) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	902 options("show.error.messages"=T)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	903 mess = paste('Fatal error: Supplied subject id list',paste(subjects,collapse=','),
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	904 'has length',nsubj,'but there are',nsamples,'samples',paste(snames,collapse=','))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	905 write(mess, stderr())
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	906 quit(save="no",status=4)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	907 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	908 if (length(subjects) != 0) {subjects = subjects[useCols]}
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	909 Count_Matrix = Count_Matrix[,useCols] ### reorder columns
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	910 rn = rownames(Count_Matrix)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	911 islib = rn %in% c('librarySize','NotInBedRegions')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	912 LibSizes = Count_Matrix[subset(rn,islib),][1] # take first
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	913 Count_Matrix = Count_Matrix[subset(rn,! islib),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	914 group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) ) #Build a group descriptor
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	915 group = factor(group, levels=c(ControlName,TreatmentName))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	916 colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_") #Relable columns
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	917 results = edgeIt(Count_Matrix=Count_Matrix,group=group, out_edgeR=out_edgeR, out_Voom=out_Voom, out_DESeq2=out_DESeq2,
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	918 fdrtype='BH',mydesign=NULL,priordf=edgeR_priordf,fdrthresh=fdrthresh,outputdir='.',
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	919 myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=subjects,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	920 doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	921 histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType,robust_meth=edgeR_robust_meth)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	922 sessionInfo()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	923 ]]>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	924 </configfile>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	925 </configfiles>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	926 <help>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	927
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	928 What it does
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	929
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	930 Allows short read sequence counts from controlled experiments to be analysed for differentially expressed genes.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	931 Optionally adds a term for subject if not all samples are independent or if some other factor needs to be blocked in the design.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	932
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	933 Input
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	934
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	935 Requires a count matrix as a tabular file. These are best made using the companion HTSeq_ based counter Galaxy wrapper
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	936 and your fave gene model to generate inputs. Each row is a genomic feature (gene or exon eg) and each column the
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	937 non-negative integer count of reads from one sample overlapping the feature.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	938 The matrix must have a header row uniquely identifying the source samples, and unique row names in
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	939 the first column. Typically the row names are gene symbols or probe ids for downstream use in GSEA and other methods.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	940
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	941 Specifying comparisons
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	942
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	943 This is basically dumbed down for two factors - case vs control.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	944
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	945 More complex interfaces are possible but painful at present.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	946 Probably need to specify a phenotype file to do this better.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	947 Work in progress. Send code.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	948
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	949 If you have (eg) paired samples and wish to include a term in the GLM to account for some other factor (subject in the case of paired samples),
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	950 put a comma separated list of indicators for every sample (whether modelled or not!) indicating (eg) the subject number or
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	951 A list of integers, one for each subject or an empty string if samples are all independent.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	952 If not empty, there must be exactly as many integers in the supplied integer list as there are columns (samples) in the count matrix.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	953 Integers for samples that are not in the analysis must be present in the string as filler even if not used.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	954
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	955 So if you have 2 pairs out of 6 samples, you need to put in unique integers for the unpaired ones
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	956 eg if you had 6 samples with the first two independent but the second and third pairs each being from independent subjects. you might use
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	957 8,9,1,1,2,2
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	958 as subject IDs to indicate two paired samples from the same subject in columns 3/4 and 5/6
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	959
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	960 Methods available
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	961
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	962 You can run 3 popular Bioconductor packages available for count data.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	963
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	964 edgeR - see edgeR_ for details
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	965
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	966 VOOM/limma - see limma_VOOM_ for details
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	967
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	968 DESeq2 - see DESeq2_ for details
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	969
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	970 and optionally camera in edgeR which works better if MSigDB is installed.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	971
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	972 Outputs
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	973
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	974 Some helpful plots and analysis results. Note that most of these are produced using R code
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	975 suggested by the excellent documentation and vignettes for the Bioconductor
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	976 packages invoked. The Tool Factory is used to automatically lay these out for you to enjoy.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	977
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	978 Note on Voom
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	979
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	980 The voom from limma version 3.16.6 help in R includes this from the authors - but you should read the paper to interpret this method.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	981
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	982 This function is intended to process RNA-Seq or ChIP-Seq data prior to linear modelling in limma.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	983
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	984 voom is an acronym for mean-variance modelling at the observational level.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	985 The key concern is to estimate the mean-variance relationship in the data, then use this to compute appropriate weights for each observation.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	986 Count data almost show non-trivial mean-variance relationships. Raw counts show increasing variance with increasing count size, while log-counts typically show a decreasing mean-variance trend.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	987 This function estimates the mean-variance trend for log-counts, then assigns a weight to each observation based on its predicted variance.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	988 The weights are then used in the linear modelling process to adjust for heteroscedasticity.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	989
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	990 In an experiment, a count value is observed for each tag in each sample. A tag-wise mean-variance trend is computed using lowess.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	991 The tag-wise mean is the mean log2 count with an offset of 0.5, across samples for a given tag.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	992 The tag-wise variance is the quarter-root-variance of normalized log2 counts per million values with an offset of 0.5, across samples for a given tag.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	993 Tags with zero counts across all samples are not included in the lowess fit. Optional normalization is performed using normalizeBetweenArrays.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	994 Using fitted values of log2 counts from a linear model fit by lmFit, variances from the mean-variance trend were interpolated for each observation.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	995 This was carried out by approxfun. Inverse variance weights can be used to correct for mean-variance trend in the count data.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	996
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	997
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	998 Author(s)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	999
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1000 Charity Law and Gordon Smyth
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1001
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1002 References
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1003
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1004 Law, CW (2013). Precision weights for gene expression analysis. PhD Thesis. University of Melbourne, Australia.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1005
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1006 Law, CW, Chen, Y, Shi, W, Smyth, GK (2013). Voom! Precision weights unlock linear model analysis tools for RNA-seq read counts.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1007 Technical Report 1 May 2013, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Reseach, Melbourne, Australia.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1008 http://www.statsci.org/smyth/pubs/VoomPreprint.pdf
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1009
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1010 See Also
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1011
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1012 A voom case study is given in the edgeR User's Guide.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1013
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1014 vooma is a similar function but for microarrays instead of RNA-seq.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1015
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1016
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1017 *old rant on changes to Bioconductor package variable names between versions*
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1018
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1019 The edgeR authors made a small cosmetic change in the name of one important variable (from p.value to PValue)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1020 breaking this and all other code that assumed the old name for this variable,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1021 between edgeR2.4.4 and 2.4.6 (the version for R 2.14 as at the time of writing).
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1022 This means that all code using edgeR is sensitive to the version. I think this was a very unwise thing
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1023 to do because it wasted hours of my time to track down and will similarly cost other edgeR users dearly
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1024 when their old scripts break. This tool currently now works with 2.4.6.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1025
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1026 Note on prior.N
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1027
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1028 http://seqanswers.com/forums/showthread.php?t=5591 says:
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1029
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1030 prior.n
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1031
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1032 The value for prior.n determines the amount of smoothing of tagwise dispersions towards the common dispersion.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1033 You can think of it as like a "weight" for the common value. (It is actually the weight for the common likelihood
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1034 in the weighted likelihood equation). The larger the value for prior.n, the more smoothing, i.e. the closer your
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1035 tagwise dispersion estimates will be to the common dispersion. If you use a prior.n of 1, then that gives the
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1036 common likelihood the weight of one observation.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1037
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1038 In answer to your question, it is a good thing to squeeze the tagwise dispersions towards a common value,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1039 or else you will be using very unreliable estimates of the dispersion. I would not recommend using the value that
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1040 you obtained from estimateSmoothing()---this is far too small and would result in virtually no moderation
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1041 (squeezing) of the tagwise dispersions. How many samples do you have in your experiment?
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1042 What is the experimental design? If you have few samples (less than 6) then I would suggest a prior.n of at least 10.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1043 If you have more samples, then the tagwise dispersion estimates will be more reliable,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1044 so you could consider using a smaller prior.n, although I would hesitate to use a prior.n less than 5.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1045
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1046
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1047 From Bioconductor Digest, Vol 118, Issue 5, Gordon writes:
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1048
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1049 Dear Dorota,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1050
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1051 The important settings are prior.df and trend.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1052
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1053 prior.n and prior.df are related through prior.df = prior.n * residual.df,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1054 and your experiment has residual.df = 36 - 12 = 24. So the old setting of
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1055 prior.n=10 is equivalent for your data to prior.df = 240, a very large
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1056 value. Going the other way, the new setting of prior.df=10 is equivalent
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1057 to prior.n=10/24.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1058
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1059 To recover old results with the current software you would use
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1060
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1061 estimateTagwiseDisp(object, prior.df=240, trend="none")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1062
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1063 To get the new default from old software you would use
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1064
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1065 estimateTagwiseDisp(object, prior.n=10/24, trend=TRUE)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1066
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1067 Actually the old trend method is equivalent to trend="loess" in the new
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1068 software. You should use plotBCV(object) to see whether a trend is
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1069 required.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1070
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1071 Note you could also use
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1072
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1073 prior.n = getPriorN(object, prior.df=10)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1074
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1075 to map between prior.df and prior.n.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1076
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1077 ----
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1078
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1079 Attributions
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1080
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1081 edgeR - edgeR_
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1082
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1083 VOOM/limma - limma_VOOM_
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1084
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1085 DESeq2 - DESeq2_ for details
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1086
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1087 See above for Bioconductor package documentation for packages exposed in Galaxy by this tool and app store package.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1088
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1089 Galaxy_ (that's what you are using right now!) for gluing everything together
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1090
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1091 Otherwise, all code and documentation comprising this tool was written by Ross Lazarus and is
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1092 licensed to you under the LGPL_ like other rgenetics artefacts
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1093
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1094 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1095 .. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1096 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1097 .. _DESeq2: http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1098 .. _limma_VOOM: http://www.bioconductor.org/packages/release/bioc/html/limma.html
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1099 .. _Galaxy: http://getgalaxy.org
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1100 </help>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1101
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1102 </tool>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1103
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	1104

Mercurial > repos > fubar > differential_count_models

annotate rgedgeRpaired_nocamera.xml @ 114:616c780f69a6 draft