differential_count_models: rgedgeRpaired

annotate rgedgeRpaired_nocamera.xml @ 127:23afddb3d1e5 draft

Uploaded

author	fubar
date	Thu, 27 Nov 2014 18:39:15 -0500
parents	731315bd6e48
children	999d4b5939bb

rev	line source
119 acbc181e918c Uploaded fubar parents: 116 diff changeset	1 <tool id="rgdifferentialcount" name="Differential_Count" version="0.27">
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>
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	4 <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	5 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
120 ee3aa2b01623 Uploaded fubar parents: 119 diff changeset	6 <requirement type="package" version="9.10">ghostscript</requirement>
115 badcd3b0e708 Uploaded fubar parents: 111 diff changeset	7 <requirement type="package" version="2.14">biocbasics</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	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">
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	11 rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "Differential_Counts"
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	12 --output_dir "$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"
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	25 multiple="true" use_header_names="true" size="120" display="checkboxes" force_select="True">
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	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"
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	30 multiple="true" use_header_names="true" size="120" display="checkboxes" force_select="True">
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	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 <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	89 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	90 <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	91 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	92 <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	93 <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	94 <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	95 <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	96 <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	97 <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	98 <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	99 <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	100 </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	101 </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	102 <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	103 <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	104 <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	105 </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	106 <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	107 <filter>DESeq2['doDESeq2'] == "T"</filter>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	108 </data>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	109 <data format="tabular" name="out_VOOM" label="${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	110 <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	111 </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	112 <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	113 </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	114 <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	115 <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	116 </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	117 <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	118 <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	119 <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	120 <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	121 <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	122 <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	123 <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	124 <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	125 <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	126 <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	127 <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	128 <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	129 <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	130 <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	131 <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	132 <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	133 <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	134 <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	135 <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	136 </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	137 </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	138
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 <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	140 <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	141 <![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	142 #
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 # 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	144 # 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	145 # 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	146 # 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	147 #
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 # 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	149 #
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 # 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	151
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 # 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	153 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	154 reallysmall = log10(.Machine\$double.xmin)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	155 library("stringr")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	156 library("gplots")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	157 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	158 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	159 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 # 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	161 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	162 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	163 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	164 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	165 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	166 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	167 } 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	168 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	169 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	170 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	171 # 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	172 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	173 # 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	174 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	175 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	176 #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	177 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	179 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	180 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	181 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	182 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	183 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	184 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	187 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 # 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	189 #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	190 #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	191 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	192 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	193 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	194 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	195 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	196 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	197 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	198 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	199 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	201 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	202 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	203 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	204 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	205 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	208 # 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	209 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	211 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	212 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	213 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	214 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	215 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	216 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	217 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	218 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	219 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	220 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	221 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	222 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	223 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	225 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	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 pdf(outSmear)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	228 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	229 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	230 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	231 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 boxPlot = function(rawrs,cleanrs,maint,myTitle,pdfname)
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	234 {
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	235 nc = ncol(rawrs)
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	236 ##### for (i in c(1:nc)) {rawrs[(rawrs[,i] < 0),i] = NA}
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	237 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	238 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	239 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	240 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	241 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	242 defpar = par(no.readonly=T)
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	243 print.noquote('@@@ Raw contig counts by 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	244 print.noquote(summary(rawrs))
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	245 print.noquote('@@@ Library size contig counts by 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	246 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	247 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	248 par(mfrow=c(1,2))
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	249 boxplot(rawrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main='log2 raw counts')
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	250 grid(col="lightgray",lty="dotted")
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	251 boxplot(cleanrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('log2 counts after ',maint))
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	252 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	253 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	254 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	255 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	256 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	257 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	258 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	259 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	260 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	261 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	262 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	263 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	265 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	266 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	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 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	269 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	270 } 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	271 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	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 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	274 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	275 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	276 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	277 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	279 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	280
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	284 { # updated to use ecdf
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	285 pdfname = "Differential_rowsum_bar_charts.pdf"
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	286 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	287 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	288 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	289 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	290 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	291 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	292 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	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 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	295 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	296 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	297 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	298 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	299 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	300 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	303 { # 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	304 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	305 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	306 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	307 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	308 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	309 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	310 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	311 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	312 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	313 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	314 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	315 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	316 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	317 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	318 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	319 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	324 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	325 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	326 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	328 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	329 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	330 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	332 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	333 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	335 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	337 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	338 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	339 } 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	340 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	341 } # 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	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 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	344 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	345 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	346 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	347 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	348 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	349 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	350 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	351 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	352 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	353 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	354 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	355 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	356 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	357 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	358 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	359 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	360 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	361 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	362 ### 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	363 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	364 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	365 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	366 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	367 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	368 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	370 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	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 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	376 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	377 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	378 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	379 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	380 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	381 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	382 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	383 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	384 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	385 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	386 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	387 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	388 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	389 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	390 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	396 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	397 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	398 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	400 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	401 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	402 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	404 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	405 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	407 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	409 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	410 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	411 } 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	412 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	413 } # 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	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 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	416 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	417 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	418 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	419 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	420 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	421 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	422 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	423 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	424 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	425 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	426 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	427 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	428 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	429 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	430 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	431 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	432 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	433 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	434 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	435 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	436 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	437 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	438 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	439 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	440 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	443 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	444 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	445 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	446 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	447 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	448 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	449 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	450 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	451 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	452 } 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	453 { 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	454 } 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	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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	460 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	461 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	462 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	463 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	464 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	465 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	466 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	467 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	468 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	469 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	470 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	471 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	472 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	473 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	474 }
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	475
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	476
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	477 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	478 fdrthresh=0.05,outputdir='.', myTitle='Differential Counts',libSize=c(),useNDF=F,
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	479 filterquantile=0.2, subjects=c(),TreatmentName="Rx",ControlName="Ctrl",mydesign=NULL,
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	480 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	481 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	482 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	483 {
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	484
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	485 logf = file('Differential.log', open = "a")
731315bd6e48 Uploaded fubar parents: 123 diff changeset	486 sink(logf,type = c("output", "message"))
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	487
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	488
731315bd6e48 Uploaded fubar parents: 123 diff changeset	489 run_edgeR = function(workCM,pdata,subjects,group,priordf,robust_meth,mydesign,mt,cmrowsums,out_edgeR,nonzerod)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	490 {
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	491 logf = file('edgeR.log', open = "a")
731315bd6e48 Uploaded fubar parents: 123 diff changeset	492 sink(logf,type = c("output", "message"))
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	493 #### Setup myDGEList object
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	494 myDGEList = DGEList(counts=workCM, group = group)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	495 myDGEList = calcNormFactors(myDGEList)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	496 if (robust_meth == 'ordinary') {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	497 myDGEList = estimateGLMCommonDisp(myDGEList,mydesign)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	498 myDGEList = estimateGLMTrendedDisp(myDGEList,mydesign)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	499 if (priordf > 0) { myDGEList = estimateGLMTagwiseDisp(myDGEList,mydesign,prior.df = priordf)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	500 } else { myDGEList = estimateGLMTagwiseDisp(myDGEList,mydesign) }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	501 comdisp = myDGEList\$common.dispersion
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	502 estpriorn = getPriorN(myDGEList)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	503 print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	504 } else {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	505 myDGEList = estimateGLMRobustDisp(myDGEList,design=mydesign, prior.df = priordf, maxit = 6, residual.type = robust_meth)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	506 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	507
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	508
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	509 DGLM = glmFit(myDGEList,design=mydesign)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	510 DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed
123 51f998262ada Uploaded fubar parents: 122 diff changeset	511 normData = cpm(myDGEList)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	512 uoutput = cbind(
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	513 Name=as.character(rownames(myDGEList\$counts)),
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	514 DE\$table,
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	515 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	516 Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums,normData,
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	517 myDGEList\$counts
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	518 )
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	519 soutput = uoutput[order(DE\$table\$PValue),] # sorted into p value order - for quick toptable
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	520 goodness = gof(DGLM, pcutoff=fdrthresh)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	521 if (sum(goodness\$outlier) > 0) {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	522 print.noquote('GLM outliers:')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	523 print(paste(rownames(DGLM)[(goodness\$outlier)],collapse=','),quote=F)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	524 } else {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	525 print('No GLM fit outlier genes found\n')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	526 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	527 z = limma::zscoreGamma(goodness\$gof.statistic, shape=goodness\$df/2, scale=2)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	528 pdf(paste("edgeR",mt,"GoodnessofFit.pdf",sep='_'))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	529 qq = qqnorm(z, panel.first=grid(), main="tagwise dispersion")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	530 abline(0,1,lwd=3)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	531 points(qq\$x[goodness\$outlier],qq\$y[goodness\$outlier], pch=16, col="maroon")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	532 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	533 uniqueg = unique(group)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	534 write.table(soutput,file=out_edgeR, quote=FALSE, sep="\t",row.names=F)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	535 tt = cbind(
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	536 Name=as.character(rownames(myDGEList)),
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	537 DE\$table,
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	538 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	539 Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	540 )
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	541 print.noquote("@@ edgeR Top tags\n")
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	542 tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	543 print.noquote(tt[1:50,])
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	544 deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,])
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	545 nsig = length(deTags)
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	546 print.noquote(paste('@@',nsig,'tags significant at adj p=',fdrthresh))
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	547 deColours = ifelse(deTags,'red','black')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	548 pdf(paste("edgeR",mt,"BCV_vs_abundance.pdf",sep="_"))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	549 plotBCV(myDGEList, cex=0.3, main="Biological CV vs abundance")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	550 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	551 dg = myDGEList[order(DE\$table\$PValue),]
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	552 outpdfname= paste("edgeR",mt,"top_100_heatmap.pdf",sep="_")
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	553 ocpm = normData[order(DE\$table\$PValue),]
731315bd6e48 Uploaded fubar parents: 123 diff changeset	554 ocpm = ocpm[c(1:100),]
731315bd6e48 Uploaded fubar parents: 123 diff changeset	555 hmap2(ocpm,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste(myTitle,'Heatmap'))
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	556 outSmear = paste("edgeR",mt,"smearplot.pdf",sep="_")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	557 outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	558 smearPlot(myDGEList=myDGEList,deTags=deTags, outSmear=outSmear, outMain = outMain)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	559 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	560 topresults.edgeR = soutput[which(soutput\$adj.p.value < fdrthresh), ]
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	561 edgeRcountsindex = which(allgenes %in% rownames(topresults.edgeR))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	562 edgeRcounts = rep(0, length(allgenes))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	563 edgeRcounts[edgeRcountsindex] = 1 # Create venn diagram of hits
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	564 sink()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	565 return(list(myDGEList=myDGEList,edgeRcounts=edgeRcounts))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	566 } ### run_edgeR
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	567
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	568
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	569 run_DESeq2 = function(workCM,pdata,subjects,group,out_DESeq2,mt,DESeq_fitType)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	570
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	571 {
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	572 logf = file("DESeq2.log", open = "a")
731315bd6e48 Uploaded fubar parents: 123 diff changeset	573 sink(logf,type = c("output", "message"))
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	574 # DESeq2
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	575 require('DESeq2')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	576 library('RColorBrewer')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	577 if (length(subjects) == 0)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	578 {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	579 pdata = data.frame(Name=colnames(workCM),Rx=group,row.names=colnames(workCM))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	580 deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ Rx))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	581 } else {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	582 pdata = data.frame(Name=colnames(workCM),Rx=group,subjects=subjects,row.names=colnames(workCM))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	583 deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ subjects + Rx))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	584 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	585 deSeqDatsizefac = estimateSizeFactors(deSEQds)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	586 deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	587 resDESeq = nbinomWaldTest(deSeqDatdisp)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	588 rDESeq = as.data.frame(results(resDESeq))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	589 rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums,URL=contigurls)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	590 srDESeq = rDESeq[order(rDESeq\$pvalue),]
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	591 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	592 cat("# DESeq top 50\n")
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	593 print.noquote(srDESeq[1:50,])
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	594 write.table(srDESeq,file=out_DESeq2, quote=FALSE, sep="\t",row.names=F)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	595 topresults.DESeq = rDESeq[which(rDESeq\$padj < fdrthresh), ]
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	596 DESeqcountsindex = which(allgenes %in% rownames(topresults.DESeq))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	597 DESeqcounts = rep(0, length(allgenes))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	598 DESeqcounts[DESeqcountsindex] = 1
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	599 pdf(paste("DESeq2",mt,"dispersion_estimates.pdf",sep='_'))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	600 plotDispEsts(resDESeq)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	601 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	602 ysmall = abs(min(rDESeq\$log2FoldChange))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	603 ybig = abs(max(rDESeq\$log2FoldChange))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	604 ylimit = min(4,ysmall,ybig)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	605 pdf(paste("DESeq2",mt,"MA_plot.pdf",sep="_"))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	606 plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	607 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	608 rlogres = rlogTransformation(resDESeq)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	609 sampledists = dist( t( assay(rlogres) ) )
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	610 sdmat = as.matrix(sampledists)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	611 pdf(paste("DESeq2",mt,"sample_distance_plot.pdf",sep="_"))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	612 heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"),
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	613 col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	614 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	615 result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) )
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	616 if ("try-error" %in% class(result)) {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	617 print.noquote('DESeq2 plotPCA failed.')
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	618 } else {
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	619 pdf(paste("DESeq2",mt,"PCA_plot.pdf",sep="_"))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	620 #### wtf - print? Seems needed to get this to work
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	621 print(ppca)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	622 dev.off()
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	623 }
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	624 sink()
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	625 return(DESeqcounts)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	626 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	627
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	628
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	629 run_Voom = function(workCM,pdata,subjects,group,mydesign,mt,out_Voom)
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	630 {
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	631 logf = file('VOOM.log', open = "a")
731315bd6e48 Uploaded fubar parents: 123 diff changeset	632 sink(logf,type = c("output", "message"))
731315bd6e48 Uploaded fubar parents: 123 diff changeset	633 if (doedgeR == F) {
731315bd6e48 Uploaded fubar parents: 123 diff changeset	634 #### Setup myDGEList object
731315bd6e48 Uploaded fubar parents: 123 diff changeset	635 myDGEList = DGEList(counts=workCM, group = group)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	636 myDGEList = calcNormFactors(myDGEList)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	637 myDGEList = estimateGLMCommonDisp(myDGEList,mydesign)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	638 myDGEList = estimateGLMTrendedDisp(myDGEList,mydesign)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	639 myDGEList = estimateGLMTagwiseDisp(myDGEList,mydesign)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	640 }
731315bd6e48 Uploaded fubar parents: 123 diff changeset	641 pdf(paste("VOOM",mt,"mean_variance_plot.pdf",sep='_'))
731315bd6e48 Uploaded fubar parents: 123 diff changeset	642 dat.voomed <- voom(myDGEList, mydesign, plot = TRUE, normalize.method="quantil", lib.size = NULL)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	643 dev.off()
731315bd6e48 Uploaded fubar parents: 123 diff changeset	644 # Use limma to fit data
731315bd6e48 Uploaded fubar parents: 123 diff changeset	645 fit = lmFit(dat.voomed, mydesign)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	646 fit = eBayes(fit)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	647 rvoom = topTable(fit, coef = length(colnames(mydesign)), adj = fdrtype, n = Inf, sort="none")
731315bd6e48 Uploaded fubar parents: 123 diff changeset	648 qqPlot(descr=paste(myTitle,'VOOM-limma adj p QQ plot'),pvector=rvoom\$adj.P.Val,outpdf=paste('VOOM',mt,'qqplot.pdf',sep='_'))
731315bd6e48 Uploaded fubar parents: 123 diff changeset	649 rownames(rvoom) = rownames(workCM)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	650 rvoom = cbind(Contig=rownames(workCM),rvoom,NReads=cmrowsums,URL=contigurls)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	651 srvoom = rvoom[order(rvoom\$P.Value),]
731315bd6e48 Uploaded fubar parents: 123 diff changeset	652 cat("# VOOM top 50\n")
731315bd6e48 Uploaded fubar parents: 123 diff changeset	653 print(srvoom[1:50,])
731315bd6e48 Uploaded fubar parents: 123 diff changeset	654 write.table(srvoom,file=out_Voom, quote=FALSE, sep="\t",row.names=F)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	655 # Use an FDR cutoff to find interesting samples for edgeR, DESeq and voom/limma
731315bd6e48 Uploaded fubar parents: 123 diff changeset	656 topresults.voom = rvoom[which(rvoom\$adj.P.Val < fdrthresh), ]
731315bd6e48 Uploaded fubar parents: 123 diff changeset	657 voomcountsindex <- which(allgenes %in% rownames(topresults.voom))
731315bd6e48 Uploaded fubar parents: 123 diff changeset	658 voomcounts = rep(0, length(allgenes))
731315bd6e48 Uploaded fubar parents: 123 diff changeset	659 voomcounts[voomcountsindex] = 1
731315bd6e48 Uploaded fubar parents: 123 diff changeset	660 sink()
731315bd6e48 Uploaded fubar parents: 123 diff changeset	661 return(voomcounts)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	662 }
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	663
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	664
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	665 #### data cleaning and analsis control starts here
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	666
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	667
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	668 # Error handling
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	669 nugroup = length(unique(group))
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	670 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	671 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	672 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	673 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	674 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	675 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	676 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	677 allN = nrow(Count_Matrix)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	678 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	679 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	680 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	681 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	682 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	683 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	684 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	685 zN = allN - nzN
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	686 print('@@@ Quantiles for non-zero row counts:',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	687 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	688 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	689 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	690 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	691 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	692 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	693 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	694 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	695 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	696 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	697 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	698 } 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	699 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	700 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	701 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	702 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	703 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	704 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	705 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	706 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	707 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	708 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	709 allgenes = rownames(workCM)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	710 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	711 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	712 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	713 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	714 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	715 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	716 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	717 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	718 } 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	719 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	720 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	721 }
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	722 print.noquote(paste("@@ Total low count contigs per sample = ",paste(table(lo),collapse=',')))
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	723 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	724 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	725 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	726 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	727 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	728 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	730 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	732 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	733 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	734 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	737 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	738 print.noquote(mydesign)
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	739 normData = cpm(workCM)*1e6
731315bd6e48 Uploaded fubar parents: 123 diff changeset	740 colnames(normData) = paste( colnames(workCM),'N',sep="_")
731315bd6e48 Uploaded fubar parents: 123 diff changeset	741 print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=',')))
731315bd6e48 Uploaded fubar parents: 123 diff changeset	742
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	743 if (doedgeR == T) {
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	744 eres = run_edgeR(workCM,pdata,subjects,group,priordf,robust_meth,mydesign,mt,cmrowsums,out_edgeR,nonzerod)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	745 myDGEList = eres\$myDGEList
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	746 edgeRcounts = eres\$edgeRcounts
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	747 #### Plot MDS
731315bd6e48 Uploaded fubar parents: 123 diff changeset	748 sample_colors = match(group,levels(group))
731315bd6e48 Uploaded fubar parents: 123 diff changeset	749 sampleTypes = levels(factor(group))
731315bd6e48 Uploaded fubar parents: 123 diff changeset	750 print.noquote(sampleTypes)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	751 pdf(paste("edgeR",mt,"MDSplot.pdf",sep='_'))
731315bd6e48 Uploaded fubar parents: 123 diff changeset	752 plotMDS.DGEList(myDGEList,main=paste("MDS for",myTitle),cex=0.5,col=sample_colors,pch=sample_colors)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	753 legend(x="topleft", legend = sampleTypes,col=c(1:length(sampleTypes)), pch=19)
731315bd6e48 Uploaded fubar parents: 123 diff changeset	754 grid(col="blue")
731315bd6e48 Uploaded fubar parents: 123 diff changeset	755 dev.off()
731315bd6e48 Uploaded fubar parents: 123 diff changeset	756 scale <- myDGEList\$samples\$lib.size*myDGEList\$samples\$norm.factors
731315bd6e48 Uploaded fubar parents: 123 diff changeset	757 normCounts <- round(t(t(myDGEList\$counts)/scale)*mean(scale))
731315bd6e48 Uploaded fubar parents: 123 diff changeset	758 try({boxPlot(rawrs=nzd,cleanrs=log2(normCounts+1),maint='Effects of TMM size normalisation',myTitle=myTitle,pdfname=paste("edgeR",mt,"raw_norm_counts_box.pdf",sep='_'))},T)
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	759 }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	760 if (doDESeq2 == T) { DESeqcounts = run_DESeq2(workCM,pdata,subjects,group,out_DESeq2,mt,DESeq_fitType) }
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	761 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	762
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	764 if (doCamera) {
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	765 doGSEA(y=myDGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle,
9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	766 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	767 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	769 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	770 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	771 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	772 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	773 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	774 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	775 } 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	776 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	777 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	778 } 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	779 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	780 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	781 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 (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	784 counts.venn = vennCounts(counts.dataframe)
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	785 vennf = paste("Differential_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	786 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	787 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	788 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	789 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 } #### doDESeq2 or doVoom
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	791 sink()
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	792 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 #### Done
121 d69a656284f5 Uploaded fubar parents: 120 diff changeset	794 ]]>
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	795 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	796 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	797 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	798 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	799 out_DESeq2 = F
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	800 out_Voom = "$out_VOOM"
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	801 edgeR_robust_meth = "ordinary"
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 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	803 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	804 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	805 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	806 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	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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 #if $doVoom == "T":
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	810 out_Voom = "$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	811 #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	812
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 #if $DESeq2.doDESeq2 == "T":
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	814 out_DESeq2 = "$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	815 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	816 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	817 #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	818
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 #if $edgeR.doedgeR == "T":
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	820 out_edgeR = "$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	821 edgeR_priordf = $edgeR.edgeR_priordf
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	822 edgeR_robust_meth = "$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	823 #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	824
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	825
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	827 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	829 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	830 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 Out_Dir = "$html_file.files_path"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	833 Input = "$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	834 TreatmentName = "$treatment_name"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	835 TreatmentCols = "$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	836 ControlName = "$control_name"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	837 ControlCols= "$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	838 org = "$input1.dbkey"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	839 if (org == "") { org = "hg19"}
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	840 fdrtype = "$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	841 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	842 useNDF = $useNDF
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	843 fQ = $fQ # non-differential centile cutoff
108 96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful fubar parents: diff changeset	844 myTitle = "$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	845 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	846 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	847 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	848 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	849 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	850 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	851 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	852 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	853 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	854 cat('\n')
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	855 <![CDATA[
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	856 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	857 if (file.exists(Out_Dir) == F) dir.create(Out_Dir)
121 d69a656284f5 Uploaded fubar parents: 120 diff changeset	858 Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t')
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	859 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	860 nsamples = length(snames)
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	861 if (nsubj > 0 & nsubj != nsamples) {
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	862 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	863 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	864 '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	865 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	866 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	867 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 if (length(subjects) != 0) {subjects = subjects[useCols]}
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	869 Count_Matrix = Count_Matrix[,useCols] ### reorder columns
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	870 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	871 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	872 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	873 Count_Matrix = Count_Matrix[subset(rn,! islib),]
121 d69a656284f5 Uploaded fubar parents: 120 diff changeset	874 group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) )
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	875 group = factor(group, levels=c(ControlName,TreatmentName))
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	876 colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_")
111 9f2e0ec3e826 Uploaded fubar parents: 110 diff changeset	877 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	878 fdrtype='BH',mydesign=NULL,priordf=edgeR_priordf,fdrthresh=fdrthresh,outputdir='.',
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	879 myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=subjects,TreatmentName=TreatmentName,ControlName=ControlName,
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	880 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	881 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	882 sessionInfo()
121 d69a656284f5 Uploaded fubar parents: 120 diff changeset	883
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	884 sink()
731315bd6e48 Uploaded fubar parents: 123 diff changeset	885 ]]>
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	886 </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	887 </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	888 <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	889
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	891
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	893 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	894
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	896
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	898 and your fave gene model to generate inputs. Each row is a genomic feature (gene or exon eg) and each column the
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	899 non-negative integer count of reads from one sample overlapping the feature.
731315bd6e48 Uploaded fubar parents: 123 diff changeset	900
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	901 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	902 the first column. Typically the row names are gene symbols or probe ids for downstream use in GSEA and other methods.
124 731315bd6e48 Uploaded fubar parents: 123 diff changeset	903 They must be unique and R names or they will be mangled - please read the fine R docs for the rules on identifiers.
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	904
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	906
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	908
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	910 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	911 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	912
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	914 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	915 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	916 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	917 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	918
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	920 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	921 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	922 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	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 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	925
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	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 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	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 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	931
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	933
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	935
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	937
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	939 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	940 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	941
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	943
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	945
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	947
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	949 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	950 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	951 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	952 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	953
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	955 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	956 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	957 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	958 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	959 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	960
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	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 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	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 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	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 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	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 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	971 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	972 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	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 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	975
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	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 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	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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 *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	982
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	984 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	985 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	986 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	987 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	988 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	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 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	991
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	993
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	995
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	997 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	998 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	999 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	1000 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	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 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	1003 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	1004 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	1005 (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	1006 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	1007 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	1008 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	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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	1012
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	1014
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	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 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	1018 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	1019 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	1020 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	1021 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	1022
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	1024
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	1026
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	1028
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	1030
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	1032 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	1033 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	1034
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	1036
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	1038
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	1040
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 ----
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	1044
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	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 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	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 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	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 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	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 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	1054
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 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	1056 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	1057
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 .. _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	1059 .. _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	1060 .. _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	1061 .. _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	1062 .. _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	1063 .. _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	1064 </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	1065
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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 </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	1067
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit 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

Mercurial > repos > fubar > differential_count_models

annotate rgedgeRpaired_nocamera.xml @ 127:23afddb3d1e5 draft