annotate rgedgeRpaired_nocamera.xml @ 116:b0d21688db8e draft

Uploaded
author fubar
date Thu, 23 Oct 2014 18:50:38 -0400
parents badcd3b0e708
children acbc181e918c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
1 <tool id="rgDifferentialCount" name="Differential_Count" version="0.26">
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
2 <description>models using BioConductor packages</description>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
3 <requirements>
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>
115
badcd3b0e708 Uploaded
fubar
parents: 111
diff changeset
6 <requirement type="package" version="9.10">ghostscript</requirement> <package name="libxml2" version="2.9.1">
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">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
11 rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
12 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
13 </command>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
14 <inputs>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
15 <param name="input1" type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
16 help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
17 <param name="title" type="text" value="Differential Counts" size="80" label="Title for job outputs"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
18 help="Supply a meaningful name here to remind you what the outputs contain">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
19 <sanitizer invalid_char="">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
20 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
21 </sanitizer>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
22 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
23 <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
24 <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
25 multiple="true" use_header_names="true" size="120" display="checkboxes">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
26 <validator type="no_options" message="Please select at least one column."/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
27 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
28 <param name="control_name" type="text" value="Control" size="50" label="Control Name"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
29 <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
30 multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
31 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
32 <param name="subjectids" type="text" optional="true" size="120" value = ""
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
33 label="IF SUBJECTS NOT ALL INDEPENDENT! Enter comma separated strings to indicate sample labels for (eg) pairing - must be one for every column in input"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
34 help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter 'A99,C21,A99,C21'">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
35 <sanitizer>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
36 <valid initial="string.letters,string.digits"><add value="," /> </valid>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
37 </sanitizer>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
38 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
39 <param name="fQ" type="float" value="0.3" size="5" label="Non-differential contig count quantile threshold - zero to analyze all non-zero read count contigs"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
40 help="May be a good or a bad idea depending on the biology and the question. EG 0.3 = sparsest 30% of contigs with at least one read are removed before analysis"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
41 <param name="useNDF" type="boolean" truevalue="T" falsevalue="F" checked="false" size="1"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
42 label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
43 help="May be a good or a bad idea depending on the biology and the question. This was the old default. Quantile based is available as an alternative"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
44
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
45 <conditional name="edgeR">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
46 <param name="doedgeR" type="select"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
47 label="Run this model using edgeR"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
48 help="edgeR uses a negative binomial model and seems to be powerful, even with few replicates">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
49 <option value="F">Do not run edgeR</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
50 <option value="T" selected="true">Run edgeR</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
51 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
52 <when value="T">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
53 <param name="edgeR_priordf" type="integer" value="10" size="3"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
54 label="prior.df for tagwise dispersion - larger value = more squeezing of tag dispersions to common dispersion. Replaces prior.n and prior.df = prior.n * residual.df"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
55 help="10 = edgeR default. Use a larger value to 'smooth' small samples. See edgeR docs and note below"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
56 <param name="edgeR_robust_method" type="select" value="20" size="3"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
57 label="Use robust dispersion method"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
58 help="Use ordinary, anscombe or deviance robust deviance estimates">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
59 <option value="ordinary" selected="true">Use ordinary deviance estimates</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
60 <option value="deviance">Use robust deviance estimates</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
61 <option value="anscombe">use Anscombe robust deviance estimates</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
62 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
63 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
64 <when value="F"></when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
65 </conditional>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
66 <conditional name="DESeq2">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
67 <param name="doDESeq2" type="select"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
68 label="Run the same model with DESeq2 and compare findings"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
69 help="DESeq2 is an update to the DESeq package. It uses different assumptions and methods to edgeR">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
70 <option value="F" selected="true">Do not run DESeq2</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
71 <option value="T">Run DESeq2</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
72 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
73 <when value="T">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
74 <param name="DESeq_fitType" type="select">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
75 <option value="parametric" selected="true">Parametric (default) fit for dispersions</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
76 <option value="local">Local fit - this will automagically be used if parametric fit fails</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
77 <option value="mean">Mean dispersion fit- use this if you really understand what you're doing - read the fine manual linked below in the documentation</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
78 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
79 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
80 <when value="F"> </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
81 </conditional>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
82 <param name="doVoom" type="select"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
83 label="Run the same model with Voom/limma and compare findings"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
84 help="Voom uses counts per million and a precise transformation of variance so count data can be analysed using limma">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
85 <option value="F" selected="true">Do not run VOOM</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
86 <option value="T">Run VOOM</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
87 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
88 <!--
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
89 <conditional name="camera">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
90 <param name="doCamera" type="select" label="Run the edgeR implementation of Camera GSEA for up/down gene sets"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
91 help="If yes, you can choose a set of genesets to test and/or supply a gmt format geneset collection from your history">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
92 <option value="F" selected="true">Do not run GSEA tests with the Camera algorithm</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
93 <option value="T">Run GSEA tests with the Camera algorithm</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
94 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
95 <when value="T">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
96 <conditional name="gmtSource">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
97 <param name="refgmtSource" type="select"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
98 label="Use a gene set (.gmt) from your history and/or use a built-in (MSigDB etc) gene set">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
99 <option value="indexed" selected="true">Use a built-in gene set</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
100 <option value="history">Use a gene set from my history</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
101 <option value="both">Add a gene set from my history to a built in gene set</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
102 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
103 <when value="indexed">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
104 <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
105 <options from_data_table="gseaGMT_3.1">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
106 <filter type="sort_by" column="2" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
107 <validator type="no_options" message="No GMT v3.1 files are available - please install them"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
108 </options>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
109 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
110 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
111 <when value="history">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
112 <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
113 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
114 <when value="both">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
115 <param name="ownGMT" type="data" format="gseagmt" label="Select a Gene Set from your history" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
116 <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
117 <options from_data_table="gseaGMT_4">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
118 <filter type="sort_by" column="2" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
119 <validator type="no_options" message="No GMT v4 files are available - please fix tool_data_table and loc files"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
120 </options>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
121 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
122 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
123 </conditional>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
124 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
125 <when value="F">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
126 </when>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
127 </conditional>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
128 -->
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
129 <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
130 help="Conventional default value of 0.05 recommended"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
131 <param name="fdrtype" type="select" label="FDR (Type II error) control method"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
132 help="Use fdr or bh typically to control for the number of tests in a reliable way">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
133 <option value="fdr" selected="true">fdr</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
134 <option value="BH">Benjamini Hochberg</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
135 <option value="BY">Benjamini Yukateli</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
136 <option value="bonferroni">Bonferroni</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
137 <option value="hochberg">Hochberg</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
138 <option value="holm">Holm</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
139 <option value="hommel">Hommel</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
140 <option value="none">no control for multiple tests</option>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
141 </param>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
142 </inputs>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
143 <outputs>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
144 <data format="tabular" name="out_edgeR" label="${title}_topTable_edgeR.xls">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
145 <filter>edgeR['doedgeR'] == "T"</filter>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
146 </data>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
147 <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
148 <filter>DESeq2['doDESeq2'] == "T"</filter>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
149 </data>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
150 <data format="tabular" name="out_VOOM" label="${title}_topTable_VOOM.xls">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
151 <filter>doVoom == "T"</filter>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
152 </data>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
153 <data format="html" name="html_file" label="${title}.html"/>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
154 </outputs>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
155 <stdio>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
156 <exit_code range="4" level="fatal" description="Number of subject ids must match total number of samples in the input matrix" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
157 </stdio>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
158 <tests>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
159 <test>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
160 <param name='input1' value='test_bams2mx.xls' ftype='tabular' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
161 <param name='treatment_name' value='liver' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
162 <param name='title' value='edgeRtest' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
163 <param name='useNDF' value='' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
164 <param name='doedgeR' value='T' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
165 <param name='doVoom' value='T' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
166 <param name='doDESeq2' value='T' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
167 <param name='fdrtype' value='fdr' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
168 <param name='edgeR_priordf' value="8" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
169 <param name='edgeR_robust' value="ordinary" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
170 <param name='fdrthresh' value="0.05" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
171 <param name='control_name' value='heart' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
172 <param name='subjectids' value='' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
173 <param name='Control_cols' value='3,4,5,9' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
174 <param name='Treat_cols' value='2,6,7,8' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
175 <output name='out_edgeR' file='edgeRtest1out.xls' compare='diff' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
176 <output name='html_file' file='edgeRtest1out.html' compare='diff' lines_diff='20' />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
177 </test>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
178 </tests>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
179
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
180 <configfiles>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
181 <configfile name="runme">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
182 <![CDATA[
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
183 #
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
184 # edgeR.Rscript
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
185 # updated feb 2014 adding outlier-robust deviance estimate options by ross for R 3.0.2/bioc 2.13
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
186 # updated npv 2011 for R 2.14.0 and edgeR 2.4.0 by ross
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
187 # Performs DGE on a count table containing n replicates of two conditions
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
188 #
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
189 # Parameters
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
190 #
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
191 # 1 - Output Dir
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
192
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
193 # Original edgeR code by: S.Lunke and A.Kaspi
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
194 reallybig = log10(.Machine\$double.xmax)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
195 reallysmall = log10(.Machine\$double.xmin)
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
196 library("stringr")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
197 library("gplots")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
198 library("edgeR")
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
199 hmap2 = function(cmat,nsamp=100,outpdfname='heatmap2.pdf', TName='Treatment',group=NA,myTitle='title goes here')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
200 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
201 # Perform clustering for significant pvalues after controlling FWER
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
202 samples = colnames(cmat)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
203 gu = unique(group)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
204 gn = rownames(cmat)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
205 if (length(gu) == 2) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
206 col.map = function(g) {if (g==gu[1]) "#FF0000" else "#0000FF"}
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
207 pcols = unlist(lapply(group,col.map))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
208 } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
209 colours = rainbow(length(gu),start=0,end=4/6)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
210 pcols = colours[match(group,gu)] }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
211 dm = cmat[(! is.na(gn)),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
212 # remove unlabelled hm rows
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
213 nprobes = nrow(dm)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
214 # sub = paste('Showing',nprobes,'contigs ranked for evidence of differential abundance')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
215 if (nprobes > nsamp) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
216 dm =dm[1:nsamp,]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
217 #sub = paste('Showing',nsamp,'contigs ranked for evidence for differential abundance out of',nprobes,'total')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
218 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
219 newcolnames = substr(colnames(dm),1,20)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
220 colnames(dm) = newcolnames
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
221 pdf(outpdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
222 heatmap.2(dm,main=myTitle,ColSideColors=pcols,col=topo.colors(100),dendrogram="col",key=T,density.info='none',
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
223 Rowv=F,scale='row',trace='none',margins=c(8,8),cexRow=0.4,cexCol=0.5)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
224 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
225 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
226
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
227 hmap = function(cmat,nmeans=4,outpdfname="heatMap.pdf",nsamp=250,TName='Treatment',group=NA,myTitle="Title goes here")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
228 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
229 # for 2 groups only was
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
230 #col.map = function(g) {if (g==TName) "#FF0000" else "#0000FF"}
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
231 #pcols = unlist(lapply(group,col.map))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
232 gu = unique(group)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
233 colours = rainbow(length(gu),start=0.3,end=0.6)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
234 pcols = colours[match(group,gu)]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
235 nrows = nrow(cmat)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
236 mtitle = paste(myTitle,'Heatmap: n contigs =',nrows)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
237 if (nrows > nsamp) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
238 cmat = cmat[c(1:nsamp),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
239 mtitle = paste('Heatmap: Top ',nsamp,' DE contigs (of ',nrows,')',sep='')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
240 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
241 newcolnames = substr(colnames(cmat),1,20)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
242 colnames(cmat) = newcolnames
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
243 pdf(outpdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
244 heatmap(cmat,scale='row',main=mtitle,cexRow=0.3,cexCol=0.4,Rowv=NA,ColSideColors=pcols)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
245 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
246 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
247
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
248 qqPlot = function(descr='qqplot',pvector, outpdf='qqplot.pdf',...)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
249 # stolen from https://gist.github.com/703512
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
250 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
251 o = -log10(sort(pvector,decreasing=F))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
252 e = -log10( 1:length(o)/length(o) )
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
253 o[o==-Inf] = reallysmall
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
254 o[o==Inf] = reallybig
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
255 maint = descr
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
256 pdf(outpdf)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
257 plot(e,o,pch=19,cex=1, main=maint, ...,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
258 xlab=expression(Expected~~-log[10](italic(p))),
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
259 ylab=expression(Observed~~-log[10](italic(p))),
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
260 xlim=c(0,max(e)), ylim=c(0,max(o)))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
261 lines(e,e,col="red")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
262 grid(col = "lightgray", lty = "dotted")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
263 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
264 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
265
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
266 smearPlot = function(myDGEList,deTags, outSmear, outMain)
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
267 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
268 pdf(outSmear)
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
269 plotSmear(myDGEList,de.tags=deTags,main=outMain)
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
270 grid(col="lightgray", lty="dotted")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
271 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
272 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
273
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
274 boxPlot = function(rawrs,cleanrs,maint,myTitle,pdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
275 { #
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
276 nc = ncol(rawrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
277 for (i in c(1:nc)) {rawrs[(rawrs[,i] < 0),i] = NA}
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
278 fullnames = colnames(rawrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
279 newcolnames = substr(colnames(rawrs),1,20)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
280 colnames(rawrs) = newcolnames
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
281 newcolnames = substr(colnames(cleanrs),1,20)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
282 colnames(cleanrs) = newcolnames
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
283 defpar = par(no.readonly=T)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
284 print.noquote('raw contig counts by sample:')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
285 print.noquote(summary(rawrs))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
286 print.noquote('normalised contig counts by sample:')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
287 print.noquote(summary(cleanrs))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
288 pdf(pdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
289 par(mfrow=c(1,2))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
290 boxplot(rawrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('Raw:',maint))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
291 grid(col="lightgray",lty="dotted")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
292 boxplot(cleanrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('After ',maint))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
293 grid(col="lightgray",lty="dotted")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
294 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
295 pdfname = "sample_counts_histogram.pdf"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
296 nc = ncol(rawrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
297 print.noquote(paste('Using ncol rawrs=',nc))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
298 ncroot = round(sqrt(nc))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
299 if (ncroot*ncroot < nc) { ncroot = ncroot + 1 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
300 m = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
301 for (i in c(1:nc)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
302 rhist = hist(rawrs[,i],breaks=100,plot=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
303 m = append(m,max(rhist\$counts))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
304 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
305 ymax = max(m)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
306 ncols = length(fullnames)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
307 if (ncols > 20)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
308 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
309 scale = 7*ncols/20
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
310 pdf(pdfname,width=scale,height=scale)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
311 } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
312 pdf(pdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
313 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
314 par(mfrow=c(ncroot,ncroot))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
315 for (i in c(1:nc)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
316 hist(rawrs[,i], main=paste("Contig logcount",i), xlab='log raw count', col="maroon",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
317 breaks=100,sub=fullnames[i],cex=0.8,ylim=c(0,ymax))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
318 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
319 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
320 par(defpar)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
321
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
322 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
323
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
324 cumPlot = function(rawrs,cleanrs,maint,myTitle)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
325 { # updated to use ecdf
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
326 pdfname = "Filtering_rowsum_bar_charts.pdf"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
327 defpar = par(no.readonly=T)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
328 lrs = log(rawrs,10)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
329 lim = max(lrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
330 pdf(pdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
331 par(mfrow=c(2,1))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
332 hist(lrs,breaks=100,main=paste('Before:',maint),xlab="# Reads (log)",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
333 ylab="Count",col="maroon",sub=myTitle, xlim=c(0,lim),las=1)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
334 grid(col="lightgray", lty="dotted")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
335 lrs = log(cleanrs,10)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
336 hist(lrs,breaks=100,main=paste('After:',maint),xlab="# Reads (log)",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
337 ylab="Count",col="maroon",sub=myTitle,xlim=c(0,lim),las=1)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
338 grid(col="lightgray", lty="dotted")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
339 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
340 par(defpar)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
341 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
342
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
343 cumPlot1 = function(rawrs,cleanrs,maint,myTitle)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
344 { # updated to use ecdf
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
345 pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"RowsumCum.pdf",sep='_')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
346 pdf(pdfname)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
347 par(mfrow=c(2,1))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
348 lastx = max(rawrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
349 rawe = knots(ecdf(rawrs))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
350 cleane = knots(ecdf(cleanrs))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
351 cy = 1:length(cleane)/length(cleane)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
352 ry = 1:length(rawe)/length(rawe)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
353 plot(rawe,ry,type='l',main=paste('Before',maint),xlab="Log Contig Total Reads",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
354 ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
355 grid(col="blue")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
356 plot(cleane,cy,type='l',main=paste('After',maint),xlab="Log Contig Total Reads",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
357 ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
358 grid(col="blue")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
359 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
360 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
361
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
362
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
363
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
364 doGSEAold = function(y=NULL,design=NULL,histgmt="",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
365 bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
366 ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
367 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
368 sink('Camera.log')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
369 genesets = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
370 if (bigmt > "")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
371 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
372 bigenesets = readLines(bigmt)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
373 genesets = bigenesets
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
374 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
375 if (histgmt > "")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
376 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
377 hgenesets = readLines(histgmt)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
378 if (bigmt > "") {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
379 genesets = rbind(genesets,hgenesets)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
380 } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
381 genesets = hgenesets
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
382 } # use only history if no bi
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
383 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
384 print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
385 genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
386 outf = outfname
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
387 head=paste(myTitle,'edgeR GSEA')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
388 write(head,file=outfname,append=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
389 ntest=length(genesets)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
390 urownames = toupper(rownames(y))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
391 upcam = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
392 downcam = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
393 for (i in 1:ntest) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
394 gs = unlist(genesets[i])
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
395 g = gs[1] # geneset_id
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
396 u = gs[2]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
397 if (u > "") { u = paste("<a href=\'",u,"\'>",u,"</a>",sep="") }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
398 glist = gs[3:length(gs)] # member gene symbols
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
399 glist = toupper(glist)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
400 inglist = urownames %in% glist
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
401 nin = sum(inglist)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
402 if ((nin > minnin) && (nin < maxnin)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
403 ### print(paste('@@found',sum(inglist),'genes in glist'))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
404 camres = camera(y=y,index=inglist,design=design)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
405 if (! is.null(camres)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
406 rownames(camres) = g # gene set name
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
407 camres = cbind(GeneSet=g,URL=u,camres)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
408 if (camres\$Direction == "Up")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
409 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
410 upcam = rbind(upcam,camres) } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
411 downcam = rbind(downcam,camres)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
412 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
413 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
414 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
415 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
416 uscam = upcam[order(upcam\$PValue),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
417 unadjp = uscam\$PValue
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
418 uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
419 nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
420 dscam = downcam[order(downcam\$PValue),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
421 unadjp = dscam\$PValue
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
422 dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
423 ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
424 write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
425 write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
426 print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
427 write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
428 print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
429 write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
430 sink()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
431 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
432
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
433
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
434
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
435
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
436 doGSEA = function(y=NULL,design=NULL,histgmt="",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
437 bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
438 ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
439 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
440 sink('Camera.log')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
441 genesets = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
442 if (bigmt > "")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
443 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
444 bigenesets = readLines(bigmt)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
445 genesets = bigenesets
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
446 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
447 if (histgmt > "")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
448 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
449 hgenesets = readLines(histgmt)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
450 if (bigmt > "") {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
451 genesets = rbind(genesets,hgenesets)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
452 } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
453 genesets = hgenesets
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
454 } # use only history if no bi
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
455 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
456 print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
457 genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
458 outf = outfname
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
459 head=paste(myTitle,'edgeR GSEA')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
460 write(head,file=outfname,append=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
461 ntest=length(genesets)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
462 urownames = toupper(rownames(y))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
463 upcam = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
464 downcam = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
465 incam = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
466 urls = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
467 gsids = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
468 for (i in 1:ntest) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
469 gs = unlist(genesets[i])
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
470 gsid = gs[1] # geneset_id
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
471 url = gs[2]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
472 if (url > "") { url = paste("<a href=\'",url,"\'>",url,"</a>",sep="") }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
473 glist = gs[3:length(gs)] # member gene symbols
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
474 glist = toupper(glist)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
475 inglist = urownames %in% glist
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
476 nin = sum(inglist)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
477 if ((nin > minnin) && (nin < maxnin)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
478 incam = c(incam,inglist)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
479 gsids = c(gsids,gsid)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
480 urls = c(urls,url)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
481 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
482 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
483 incam = as.list(incam)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
484 names(incam) = gsids
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
485 allcam = camera(y=y,index=incam,design=design)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
486 allcamres = cbind(geneset=gsids,allcam,URL=urls)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
487 for (i in 1:ntest) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
488 camres = allcamres[i]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
489 res = try(test = (camres\$Direction == "Up"))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
490 if ("try-error" %in% class(res)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
491 cat("test failed, camres = :")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
492 print.noquote(camres)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
493 } else { if (camres\$Direction == "Up")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
494 { upcam = rbind(upcam,camres)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
495 } else { downcam = rbind(downcam,camres)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
496 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
497
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
498 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
499 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
500 uscam = upcam[order(upcam\$PValue),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
501 unadjp = uscam\$PValue
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
502 uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
503 nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
504 dscam = downcam[order(downcam\$PValue),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
505 unadjp = dscam\$PValue
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
506 dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
507 ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
508 write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
509 write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
510 print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
511 write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
512 print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
513 write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
514 sink()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
515 }
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
516
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
517
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
518 edgeIt = function (Count_Matrix=c(),group=c(),out_edgeR=F,out_Voom=F,out_DESeq2=F,fdrtype='fdr',priordf=5,
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
519 fdrthresh=0.05,outputdir='.', myTitle='Differential Counts',libSize=c(),useNDF=F,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
520 filterquantile=0.2, subjects=c(),mydesign=NULL,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
521 doDESeq2=T,doVoom=T,doCamera=T,doedgeR=T,org='hg19',
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
522 histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
523 doCook=F,DESeq_fitType="parameteric",robust_meth='ordinary')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
524 {
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
525
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
526
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
527 run_edgeR = function(workCM,pdata,subjects,group,priordf,robust_meth,mydesign,mt,cmrowsums,out_edgeR)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
528 {
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
529 sink('edgeR.log')
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
530 #### Setup myDGEList object
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
531 myDGEList = DGEList(counts=workCM, group = group)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
532 myDGEList = calcNormFactors(myDGEList)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
533 if (robust_meth == 'ordinary') {
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
534 myDGEList = estimateGLMCommonDisp(myDGEList,mydesign)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
535 myDGEList = estimateGLMTrendedDisp(myDGEList,mydesign)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
536 if (priordf > 0) { myDGEList = estimateGLMTagwiseDisp(myDGEList,mydesign,prior.df = priordf)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
537 } else { myDGEList = estimateGLMTagwiseDisp(myDGEList,mydesign) }
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
538 comdisp = myDGEList\$common.dispersion
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
539 estpriorn = getPriorN(myDGEList)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
540 print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
541 } else {
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
542 myDGEList = estimateGLMRobustDisp(myDGEList,design=mydesign, prior.df = priordf, maxit = 6, residual.type = robust_meth)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
543 }
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
544
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
545
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
546 DGLM = glmFit(myDGEList,design=mydesign)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
547 DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
548 efflib = myDGEList\$samples\$lib.size*myDGEList\$samples\$norm.factors
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
549 normData = (1e+06*myDGEList\$counts/efflib)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
550 uoutput = cbind(
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
551 Name=as.character(rownames(myDGEList\$counts)),
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
552 DE\$table,
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
553 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
554 Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums,normData,
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
555 myDGEList\$counts
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
556 )
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
557 soutput = uoutput[order(DE\$table\$PValue),] # sorted into p value order - for quick toptable
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
558 goodness = gof(DGLM, pcutoff=fdrthresh)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
559 if (sum(goodness\$outlier) > 0) {
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
560 print.noquote('GLM outliers:')
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
561 print(paste(rownames(DGLM)[(goodness\$outlier)],collapse=','),quote=F)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
562 } else {
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
563 print('No GLM fit outlier genes found\n')
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
564 }
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
565 z = limma::zscoreGamma(goodness\$gof.statistic, shape=goodness\$df/2, scale=2)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
566 pdf(paste("edgeR",mt,"GoodnessofFit.pdf",sep='_'))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
567 qq = qqnorm(z, panel.first=grid(), main="tagwise dispersion")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
568 abline(0,1,lwd=3)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
569 points(qq\$x[goodness\$outlier],qq\$y[goodness\$outlier], pch=16, col="maroon")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
570 dev.off()
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
571 uniqueg = unique(group)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
572 #### Plot MDS
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
573 sample_colors = match(group,levels(group))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
574 sampleTypes = levels(factor(group))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
575 print.noquote(sampleTypes)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
576 pdf(paste("edgeR",mt,"MDSplot.pdf",sep='_'))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
577 plotMDS.DGEList(myDGEList,main=paste("edgeR MDS for",myTitle),cex=0.5,col=sample_colors,pch=sample_colors)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
578 legend(x="topleft", legend = sampleTypes,col=c(1:length(sampleTypes)), pch=19)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
579 grid(col="blue")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
580 dev.off()
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
581 colnames(normData) = paste( colnames(normData),'N',sep="_")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
582 print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=',')))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
583 nzd = data.frame(log(nonzerod + 1e-2,10))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
584 try( boxPlot(rawrs=nzd,cleanrs=log(normData,10),maint='TMM Normalisation',myTitle=myTitle,pdfname=paste("edgeR",mt,"raw_norm_counts_box.pdf",sep='_') ))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
585 write.table(soutput,file=out_edgeR, quote=FALSE, sep="\t",row.names=F)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
586 tt = cbind(
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
587 Name=as.character(rownames(myDGEList)),
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
588 DE\$table,
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
589 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
590 Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
591 )
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
592 print.noquote("# edgeR Top tags\n")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
593 tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
594 tt = tt[order(DE\$table\$PValue),]
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
595 print.noquote(tt[1:50,])
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
596 deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,])
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
597 nsig = length(deTags)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
598 print(paste('#',nsig,'tags significant at adj p=',fdrthresh),quote=F)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
599 deColours = ifelse(deTags,'red','black')
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
600 pdf(paste("edgeR",mt,"BCV_vs_abundance.pdf",sep="_"))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
601 plotBCV(myDGEList, cex=0.3, main="Biological CV vs abundance")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
602 dev.off()
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
603 dg = myDGEList[order(DE\$table\$PValue),]
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
604 #normData = (1e+06 * dg\$counts/expandAsMatrix(dg\$samples\$lib.size, dim(dg)))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
605 outpdfname= paste("edgeR",mt,"top_100_heatmap.pdf",sep="_")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
606 hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste(myTitle,'Heatmap'))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
607 outSmear = paste("edgeR",mt,"smearplot.pdf",sep="_")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
608 outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='')
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
609 smearPlot(myDGEList=myDGEList,deTags=deTags, outSmear=outSmear, outMain = outMain)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
610 qqPlot(descr=paste(myTitle,'edgeR adj p QQ plot'),pvector=tt\$adj.p.value,outpdf=paste('edgeR',mt,'qqplot.pdf',sep='_'))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
611 norm.factor = myDGEList\$samples\$norm.factors
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
612 topresults.edgeR = soutput[which(soutput\$adj.p.value < fdrthresh), ]
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
613 edgeRcountsindex = which(allgenes %in% rownames(topresults.edgeR))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
614 edgeRcounts = rep(0, length(allgenes))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
615 edgeRcounts[edgeRcountsindex] = 1 # Create venn diagram of hits
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
616 sink()
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
617 return(list(myDGEList=myDGEList,edgeRcounts=edgeRcounts))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
618 } ### run_edgeR
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
619
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
620
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
621 run_DESeq2 = function(workCM,pdata,subjects,group,out_DESeq2,mt,DESeq_fitType)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
622
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
623 {
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
624 sink("DESeq2.log")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
625 # DESeq2
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
626 require('DESeq2')
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
627 library('RColorBrewer')
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
628 if (length(subjects) == 0)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
629 {
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
630 pdata = data.frame(Name=colnames(workCM),Rx=group,row.names=colnames(workCM))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
631 deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ Rx))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
632 } else {
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
633 pdata = data.frame(Name=colnames(workCM),Rx=group,subjects=subjects,row.names=colnames(workCM))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
634 deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ subjects + Rx))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
635 }
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
636 #DESeq2 = DESeq(deSEQds,fitType='local',pAdjustMethod=fdrtype)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
637 #rDESeq = results(DESeq2)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
638 #newCountDataSet(workCM, group)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
639 deSeqDatsizefac = estimateSizeFactors(deSEQds)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
640 deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
641 resDESeq = nbinomWaldTest(deSeqDatdisp)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
642 rDESeq = as.data.frame(results(resDESeq))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
643 rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums,URL=contigurls)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
644 srDESeq = rDESeq[order(rDESeq\$pvalue),]
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
645 qqPlot(descr=paste(myTitle,'DESeq2 adj p qq plot'),pvector=rDESeq\$padj,outpdf=paste('DESeq2',mt,'qqplot.pdf',sep="_"))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
646 cat("# DESeq top 50\n")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
647 print.noquote(srDESeq[1:50,])
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
648 write.table(srDESeq,file=out_DESeq2, quote=FALSE, sep="\t",row.names=F)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
649 topresults.DESeq = rDESeq[which(rDESeq\$padj < fdrthresh), ]
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
650 DESeqcountsindex = which(allgenes %in% rownames(topresults.DESeq))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
651 DESeqcounts = rep(0, length(allgenes))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
652 DESeqcounts[DESeqcountsindex] = 1
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
653 pdf(paste("DESeq2",mt,"dispersion_estimates.pdf",sep='_'))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
654 plotDispEsts(resDESeq)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
655 dev.off()
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
656 ysmall = abs(min(rDESeq\$log2FoldChange))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
657 ybig = abs(max(rDESeq\$log2FoldChange))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
658 ylimit = min(4,ysmall,ybig)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
659 pdf(paste("DESeq2",mt,"MA_plot.pdf",sep="_"))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
660 plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
661 dev.off()
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
662 rlogres = rlogTransformation(resDESeq)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
663 sampledists = dist( t( assay(rlogres) ) )
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
664 sdmat = as.matrix(sampledists)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
665 pdf(paste("DESeq2",mt,"sample_distance_plot.pdf",sep="_"))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
666 heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"),
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
667 col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
668 dev.off()
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
669 ###outpdfname=paste("DESeq2",mt,"top50_heatmap.pdf",sep="_")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
670 ###hmap2(sresDESeq,nsamp=50,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('DESeq2 vst rlog Heatmap',myTitle))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
671 sink()
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
672 result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) )
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
673 if ("try-error" %in% class(result)) {
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
674 print.noquote('DESeq2 plotPCA failed.')
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
675 } else {
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
676 pdf(paste("DESeq2",mt,"PCA_plot.pdf",sep="_"))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
677 #### wtf - print? Seems needed to get this to work
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
678 print(ppca)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
679 dev.off()
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
680 }
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
681 return(DESeqcounts)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
682 }
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
683
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
684
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
685 run_Voom = function(workCM,pdata,subjects,group,mydesign,mt,out_Voom)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
686 {
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
687 sink('VOOM.log')
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
688 if (doedgeR == F) {
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
689 #### Setup myDGEList object
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
690 myDGEList = DGEList(counts=workCM, group = group)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
691 myDGEList = calcNormFactors(myDGEList)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
692 myDGEList = estimateGLMCommonDisp(myDGEList,mydesign)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
693 myDGEList = estimateGLMTrendedDisp(myDGEList,mydesign)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
694 myDGEList = estimateGLMTagwiseDisp(myDGEList,mydesign)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
695 }
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
696 pdf(paste("VOOM",mt,"mean_variance_plot.pdf",sep='_'))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
697 dat.voomed <- voom(myDGEList, mydesign, plot = TRUE, normalize.method="quantil", lib.size = NULL)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
698 dev.off()
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
699 # Use limma to fit data
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
700 fit = lmFit(dat.voomed, mydesign)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
701 fit = eBayes(fit)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
702 rvoom = topTable(fit, coef = length(colnames(mydesign)), adj = fdrtype, n = Inf, sort="none")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
703 qqPlot(descr=paste(myTitle,'VOOM-limma adj p QQ plot'),pvector=rvoom\$adj.P.Val,outpdf=paste('VOOM',mt,'qqplot.pdf',sep='_'))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
704 rownames(rvoom) = rownames(workCM)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
705 rvoom = cbind(rvoom,NReads=cmrowsums,URL=contigurls)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
706 srvoom = rvoom[order(rvoom\$P.Value),]
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
707 cat("# VOOM top 50\n")
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
708 print(srvoom[1:50,])
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
709 write.table(srvoom,file=out_Voom, quote=FALSE, sep="\t",row.names=F)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
710 # Use an FDR cutoff to find interesting samples for edgeR, DESeq and voom/limma
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
711 topresults.voom = rvoom[which(rvoom\$adj.P.Val < fdrthresh), ]
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
712 voomcountsindex <- which(allgenes %in% rownames(topresults.voom))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
713 voomcounts = rep(0, length(allgenes))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
714 voomcounts[voomcountsindex] = 1
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
715 sink()
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
716 return(voomcounts)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
717 }
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
718
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
719
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
720 #### data cleaning and analsis control starts here
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
721
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
722 # Error handling
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
723 nugroup = length(unique(group))
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
724 if (nugroup!=2){
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
725 print("Number of conditions identified in experiment does not equal 2")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
726 q()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
727 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
728 require(edgeR)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
729 options(width = 512)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
730 mt = paste(unlist(strsplit(myTitle,'_')),collapse=" ")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
731 allN = nrow(Count_Matrix)
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
732 nscut = round(ncol(Count_Matrix)/2) # half samples
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
733 colTotmillionreads = colSums(Count_Matrix)/1e6
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
734 counts.dataframe = as.data.frame(c())
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
735 rawrs = rowSums(Count_Matrix)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
736 nonzerod = Count_Matrix[(rawrs > 0),] # remove all zero count genes
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
737 nzN = nrow(nonzerod)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
738 nzrs = rowSums(nonzerod)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
739 zN = allN - nzN
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
740 print('# Quantiles for non-zero row counts:',quote=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
741 print(quantile(nzrs,probs=seq(0,1,0.1)),quote=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
742 if (useNDF == T)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
743 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
744 gt1rpin3 = rowSums(Count_Matrix/expandAsMatrix(colTotmillionreads,dim(Count_Matrix)) >= 1) >= nscut
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
745 lo = colSums(Count_Matrix[!gt1rpin3,])
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
746 workCM = Count_Matrix[gt1rpin3,]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
747 cleanrs = rowSums(workCM)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
748 cleanN = length(cleanrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
749 meth = paste( "After removing",length(lo),"contigs with fewer than ",nscut," sample read counts >= 1 per million, there are",sep="")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
750 print(paste("Read",allN,"contigs. Removed",zN,"contigs with no reads.",meth,cleanN,"contigs"),quote=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
751 maint = paste('Filter >=1/million reads in >=',nscut,'samples')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
752 } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
753 useme = (nzrs > quantile(nzrs,filterquantile))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
754 workCM = nonzerod[useme,]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
755 lo = colSums(nonzerod[!useme,])
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
756 cleanrs = rowSums(workCM)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
757 cleanN = length(cleanrs)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
758 meth = paste("After filtering at count quantile =",filterquantile,", there are",sep="")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
759 print(paste('Read',allN,"contigs. Removed",zN,"with no reads.",meth,cleanN,"contigs"),quote=F)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
760 maint = paste('Filter below',filterquantile,'quantile')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
761 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
762 cumPlot(rawrs=rawrs,cleanrs=cleanrs,maint=maint,myTitle=myTitle)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
763 allgenes = rownames(workCM)
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
764 reg = "^chr([0-9]+):([0-9]+)-([0-9]+)" # ucsc chr:start-end regexp
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
765 genecards="<a href=\'http://www.genecards.org/index.php?path=/Search/keyword/"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
766 ucsc = paste("<a href=\'http://genome.ucsc.edu/cgi-bin/hgTracks?db=",org,sep='')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
767 testreg = str_match(allgenes,reg)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
768 if (sum(!is.na(testreg[,1]))/length(testreg[,1]) > 0.8) # is ucsc style string
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
769 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
770 print("@@ using ucsc substitution for urls")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
771 contigurls = paste0(ucsc,"&amp;position=chr",testreg[,2],":",testreg[,3],"-",testreg[,4],"\'>",allgenes,"</a>")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
772 } else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
773 print("@@ using genecards substitution for urls")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
774 contigurls = paste0(genecards,allgenes,"\'>",allgenes,"</a>")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
775 }
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
776 print.noquote("# urls sample")
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
777 print.noquote(head(contigurls))
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
778 print(paste("# Total low count contigs per sample = ",table(lo)),quote=F)
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
779 cmrowsums = rowSums(workCM)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
780 TName=unique(group)[1]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
781 CName=unique(group)[2]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
782 if (is.null(mydesign)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
783 if (length(subjects) == 0)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
784 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
785 mydesign = model.matrix(~group)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
786 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
787 else {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
788 subjf = factor(subjects)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
789 mydesign = model.matrix(~subjf+group) # we block on subject so make group last to simplify finding it
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
790 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
791 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
792 print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=',')))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
793 print.noquote('Using design matrix:')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
794 print.noquote(mydesign)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
795 if (doedgeR == T) {
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
796 eres = run_edgeR(workCM,pdata,subjects,group,priordf,robust_meth,mydesign,mt,cmrowsums,out_edgeR)
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
797 myDGEList = eres\$myDGEList
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
798 edgeRcounts = eres\$edgeRcounts
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
799 }
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
800 if (doDESeq2 == T) { DESeqcounts = run_DESeq2(workCM,pdata,subjects,group,out_DESeq2,mt,DESeq_fitType) }
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
801 if (doVoom == T) { voomcounts = run_Voom(workCM,pdata,subjects,group,mydesign,mt,out_Voom) }
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
802
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
803
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
804 if (doCamera) {
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
805 doGSEA(y=myDGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle,
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
806 outfname=paste("GSEA_Camera",mt,"table.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype)
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
807 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
808 counts.dataframe = c()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
809 vennmain = 'no venn'
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
810 if ((doDESeq2==T) || (doVoom==T) || (doedgeR==T)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
811 if ((doVoom==T) && (doDESeq2==T) && (doedgeR==T)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
812 vennmain = paste(mt,'Voom,edgeR and DESeq2 overlap at FDR=',fdrthresh)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
813 counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
814 VOOM_limma = voomcounts, row.names = allgenes)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
815 } else if ((doDESeq2==T) && (doedgeR==T)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
816 vennmain = paste(mt,'DESeq2 and edgeR overlap at FDR=',fdrthresh)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
817 counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, row.names = allgenes)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
818 } else if ((doVoom==T) && (doedgeR==T)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
819 vennmain = paste(mt,'Voom and edgeR overlap at FDR=',fdrthresh)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
820 counts.dataframe = data.frame(edgeR = edgeRcounts, VOOM_limma = voomcounts, row.names = allgenes)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
821 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
822
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
823 if (nrow(counts.dataframe > 1)) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
824 counts.venn = vennCounts(counts.dataframe)
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
825 vennf = paste("Venn",mt,"significant_genes_overlap.pdf",sep="_")
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
826 pdf(vennf)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
827 vennDiagram(counts.venn,main=vennmain,col="maroon")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
828 dev.off()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
829 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
830 } #### doDESeq2 or doVoom
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
831
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
832 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
833 #### Done
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
834
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
835 ###sink(stdout(),append=T,type="message")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
836 builtin_gmt = ""
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
837 history_gmt = ""
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
838 history_gmt_name = ""
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
839 out_edgeR = F
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
840 out_DESeq2 = F
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
841 out_Voom = "$out_VOOM"
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
842 edgeR_robust_meth = "ordinary" # control robust deviance options
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
843 doDESeq2 = $DESeq2.doDESeq2
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
844 doVoom = $doVoom
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
845 doCamera = F
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
846 doedgeR = $edgeR.doedgeR
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
847 edgeR_priordf = 10
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
848
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
849
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
850 #if $doVoom == "T":
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
851 out_Voom = "$out_VOOM"
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
852 #end if
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
853
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
854 #if $DESeq2.doDESeq2 == "T":
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
855 out_DESeq2 = "$out_DESeq2"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
856 doDESeq2 = T
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
857 DESeq_fitType = "$DESeq2.DESeq_fitType"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
858 #end if
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
859
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
860 #if $edgeR.doedgeR == "T":
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
861 out_edgeR = "$out_edgeR"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
862 edgeR_priordf = $edgeR.edgeR_priordf
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
863 edgeR_robust_meth = "$edgeR.edgeR_robust_method"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
864 #end if
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
865
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
866
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
867 if (sum(c(doedgeR,doVoom,doDESeq2)) == 0)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
868 {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
869 write("No methods chosen - nothing to do! Please try again after choosing one or more methods", stderr())
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
870 quit(save="no",status=2)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
871 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
872
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
873 Out_Dir = "$html_file.files_path"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
874 Input = "$input1"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
875 TreatmentName = "$treatment_name"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
876 TreatmentCols = "$Treat_cols"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
877 ControlName = "$control_name"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
878 ControlCols= "$Control_cols"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
879 org = "$input1.dbkey"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
880 if (org == "") { org = "hg19"}
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
881 fdrtype = "$fdrtype"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
882 fdrthresh = $fdrthresh
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
883 useNDF = $useNDF
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
884 fQ = $fQ # non-differential centile cutoff
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
885 myTitle = "$title"
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
886 sids = strsplit("$subjectids",',')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
887 subjects = unlist(sids)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
888 nsubj = length(subjects)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
889 TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
890 CCols = as.numeric(strsplit(ControlCols,",")[[1]])-1
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
891 cat('Got TCols=')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
892 cat(TCols)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
893 cat('; CCols=')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
894 cat(CCols)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
895 cat('\n')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
896 useCols = c(TCols,CCols)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
897 if (file.exists(Out_Dir) == F) dir.create(Out_Dir)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
898 Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t') #Load tab file assume header
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
899 snames = colnames(Count_Matrix)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
900 nsamples = length(snames)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
901 if (nsubj > 0 & nsubj != nsamples) {
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
902 options("show.error.messages"=T)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
903 mess = paste('Fatal error: Supplied subject id list',paste(subjects,collapse=','),
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
904 'has length',nsubj,'but there are',nsamples,'samples',paste(snames,collapse=','))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
905 write(mess, stderr())
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
906 quit(save="no",status=4)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
907 }
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
908 if (length(subjects) != 0) {subjects = subjects[useCols]}
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
909 Count_Matrix = Count_Matrix[,useCols] ### reorder columns
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
910 rn = rownames(Count_Matrix)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
911 islib = rn %in% c('librarySize','NotInBedRegions')
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
912 LibSizes = Count_Matrix[subset(rn,islib),][1] # take first
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
913 Count_Matrix = Count_Matrix[subset(rn,! islib),]
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
914 group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) ) #Build a group descriptor
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
915 group = factor(group, levels=c(ControlName,TreatmentName))
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
916 colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_") #Relable columns
111
9f2e0ec3e826 Uploaded
fubar
parents: 110
diff changeset
917 results = edgeIt(Count_Matrix=Count_Matrix,group=group, out_edgeR=out_edgeR, out_Voom=out_Voom, out_DESeq2=out_DESeq2,
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
918 fdrtype='BH',mydesign=NULL,priordf=edgeR_priordf,fdrthresh=fdrthresh,outputdir='.',
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
919 myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=subjects,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
920 doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
921 histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType,robust_meth=edgeR_robust_meth)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
922 sessionInfo()
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
923 ]]>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
924 </configfile>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
925 </configfiles>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
926 <help>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
927
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
928 **What it does**
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
929
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
930 Allows short read sequence counts from controlled experiments to be analysed for differentially expressed genes.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
931 Optionally adds a term for subject if not all samples are independent or if some other factor needs to be blocked in the design.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
932
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
933 **Input**
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
934
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
935 Requires a count matrix as a tabular file. These are best made using the companion HTSeq_ based counter Galaxy wrapper
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
936 and your fave gene model to generate inputs. Each row is a genomic feature (gene or exon eg) and each column the
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
937 non-negative integer count of reads from one sample overlapping the feature.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
938 The matrix must have a header row uniquely identifying the source samples, and unique row names in
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
939 the first column. Typically the row names are gene symbols or probe ids for downstream use in GSEA and other methods.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
940
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
941 **Specifying comparisons**
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
942
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
943 This is basically dumbed down for two factors - case vs control.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
944
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
945 More complex interfaces are possible but painful at present.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
946 Probably need to specify a phenotype file to do this better.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
947 Work in progress. Send code.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
948
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
949 If you have (eg) paired samples and wish to include a term in the GLM to account for some other factor (subject in the case of paired samples),
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
950 put a comma separated list of indicators for every sample (whether modelled or not!) indicating (eg) the subject number or
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
951 A list of integers, one for each subject or an empty string if samples are all independent.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
952 If not empty, there must be exactly as many integers in the supplied integer list as there are columns (samples) in the count matrix.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
953 Integers for samples that are not in the analysis *must* be present in the string as filler even if not used.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
954
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
955 So if you have 2 pairs out of 6 samples, you need to put in unique integers for the unpaired ones
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
956 eg if you had 6 samples with the first two independent but the second and third pairs each being from independent subjects. you might use
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
957 8,9,1,1,2,2
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
958 as subject IDs to indicate two paired samples from the same subject in columns 3/4 and 5/6
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
959
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
960 **Methods available**
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
961
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
962 You can run 3 popular Bioconductor packages available for count data.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
963
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
964 edgeR - see edgeR_ for details
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
965
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
966 VOOM/limma - see limma_VOOM_ for details
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
967
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
968 DESeq2 - see DESeq2_ for details
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
969
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
970 and optionally camera in edgeR which works better if MSigDB is installed.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
971
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
972 **Outputs**
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
973
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
974 Some helpful plots and analysis results. Note that most of these are produced using R code
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
975 suggested by the excellent documentation and vignettes for the Bioconductor
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
976 packages invoked. The Tool Factory is used to automatically lay these out for you to enjoy.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
977
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
978 **Note on Voom**
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
979
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
980 The voom from limma version 3.16.6 help in R includes this from the authors - but you should read the paper to interpret this method.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
981
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
982 This function is intended to process RNA-Seq or ChIP-Seq data prior to linear modelling in limma.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
983
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
984 voom is an acronym for mean-variance modelling at the observational level.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
985 The key concern is to estimate the mean-variance relationship in the data, then use this to compute appropriate weights for each observation.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
986 Count data almost show non-trivial mean-variance relationships. Raw counts show increasing variance with increasing count size, while log-counts typically show a decreasing mean-variance trend.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
987 This function estimates the mean-variance trend for log-counts, then assigns a weight to each observation based on its predicted variance.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
988 The weights are then used in the linear modelling process to adjust for heteroscedasticity.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
989
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
990 In an experiment, a count value is observed for each tag in each sample. A tag-wise mean-variance trend is computed using lowess.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
991 The tag-wise mean is the mean log2 count with an offset of 0.5, across samples for a given tag.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
992 The tag-wise variance is the quarter-root-variance of normalized log2 counts per million values with an offset of 0.5, across samples for a given tag.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
993 Tags with zero counts across all samples are not included in the lowess fit. Optional normalization is performed using normalizeBetweenArrays.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
994 Using fitted values of log2 counts from a linear model fit by lmFit, variances from the mean-variance trend were interpolated for each observation.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
995 This was carried out by approxfun. Inverse variance weights can be used to correct for mean-variance trend in the count data.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
996
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
997
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
998 Author(s)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
999
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1000 Charity Law and Gordon Smyth
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1001
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1002 References
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1003
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1004 Law, CW (2013). Precision weights for gene expression analysis. PhD Thesis. University of Melbourne, Australia.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1005
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1006 Law, CW, Chen, Y, Shi, W, Smyth, GK (2013). Voom! Precision weights unlock linear model analysis tools for RNA-seq read counts.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1007 Technical Report 1 May 2013, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Reseach, Melbourne, Australia.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1008 http://www.statsci.org/smyth/pubs/VoomPreprint.pdf
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1009
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1010 See Also
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1011
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1012 A voom case study is given in the edgeR User's Guide.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1013
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1014 vooma is a similar function but for microarrays instead of RNA-seq.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1015
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1016
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1017 ***old rant on changes to Bioconductor package variable names between versions***
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1018
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1019 The edgeR authors made a small cosmetic change in the name of one important variable (from p.value to PValue)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1020 breaking this and all other code that assumed the old name for this variable,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1021 between edgeR2.4.4 and 2.4.6 (the version for R 2.14 as at the time of writing).
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1022 This means that all code using edgeR is sensitive to the version. I think this was a very unwise thing
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1023 to do because it wasted hours of my time to track down and will similarly cost other edgeR users dearly
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1024 when their old scripts break. This tool currently now works with 2.4.6.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1025
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1026 **Note on prior.N**
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1027
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1028 http://seqanswers.com/forums/showthread.php?t=5591 says:
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1029
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1030 *prior.n*
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1031
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1032 The value for prior.n determines the amount of smoothing of tagwise dispersions towards the common dispersion.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1033 You can think of it as like a "weight" for the common value. (It is actually the weight for the common likelihood
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1034 in the weighted likelihood equation). The larger the value for prior.n, the more smoothing, i.e. the closer your
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1035 tagwise dispersion estimates will be to the common dispersion. If you use a prior.n of 1, then that gives the
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1036 common likelihood the weight of one observation.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1037
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1038 In answer to your question, it is a good thing to squeeze the tagwise dispersions towards a common value,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1039 or else you will be using very unreliable estimates of the dispersion. I would not recommend using the value that
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1040 you obtained from estimateSmoothing()---this is far too small and would result in virtually no moderation
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1041 (squeezing) of the tagwise dispersions. How many samples do you have in your experiment?
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1042 What is the experimental design? If you have few samples (less than 6) then I would suggest a prior.n of at least 10.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1043 If you have more samples, then the tagwise dispersion estimates will be more reliable,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1044 so you could consider using a smaller prior.n, although I would hesitate to use a prior.n less than 5.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1045
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1046
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1047 From Bioconductor Digest, Vol 118, Issue 5, Gordon writes:
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1048
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1049 Dear Dorota,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1050
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1051 The important settings are prior.df and trend.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1052
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1053 prior.n and prior.df are related through prior.df = prior.n * residual.df,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1054 and your experiment has residual.df = 36 - 12 = 24. So the old setting of
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1055 prior.n=10 is equivalent for your data to prior.df = 240, a very large
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1056 value. Going the other way, the new setting of prior.df=10 is equivalent
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1057 to prior.n=10/24.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1058
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1059 To recover old results with the current software you would use
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1060
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1061 estimateTagwiseDisp(object, prior.df=240, trend="none")
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1062
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1063 To get the new default from old software you would use
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1064
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1065 estimateTagwiseDisp(object, prior.n=10/24, trend=TRUE)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1066
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1067 Actually the old trend method is equivalent to trend="loess" in the new
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1068 software. You should use plotBCV(object) to see whether a trend is
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1069 required.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1070
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1071 Note you could also use
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1072
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1073 prior.n = getPriorN(object, prior.df=10)
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1074
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1075 to map between prior.df and prior.n.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1076
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1077 ----
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1078
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1079 **Attributions**
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1080
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1081 edgeR - edgeR_
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1082
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1083 VOOM/limma - limma_VOOM_
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1084
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1085 DESeq2 - DESeq2_ for details
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1086
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1087 See above for Bioconductor package documentation for packages exposed in Galaxy by this tool and app store package.
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1088
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1089 Galaxy_ (that's what you are using right now!) for gluing everything together
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1090
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1091 Otherwise, all code and documentation comprising this tool was written by Ross Lazarus and is
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1092 licensed to you under the LGPL_ like other rgenetics artefacts
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1093
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1094 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1095 .. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1096 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1097 .. _DESeq2: http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1098 .. _limma_VOOM: http://www.bioconductor.org/packages/release/bioc/html/limma.html
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1099 .. _Galaxy: http://getgalaxy.org
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1100 </help>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1101
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1102 </tool>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1103
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
1104