Mercurial > repos > fubar > differential_count_models

annotate rgedgeRpaired_nocamera.xml @ 50:60aceade5350 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
author fubar
date Mon, 23 Dec 2013 21:36:34 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
50
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1 <tool id="rgDifferentialCount" name="Differential_Count" version="0.23">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
2 <description>models using BioConductor packages</description>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
3 <requirements>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
4 <requirement type="package" version="3.11.11">atlas</requirement>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
5 <requirement type="package" version="3.0.1">r3</requirement>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
6 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
7 <requirement type="package" version="9.07">ghostscript</requirement>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
8 <requirement type="package" version="2.12">biocbasics</requirement>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
9 </requirements>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
10
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
11 <command interpreter="python">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
12 rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
13 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
14 </command>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
15 <inputs>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
16 <param name="input1" type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
17 help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
18 <param name="title" type="text" value="Differential Counts" size="80" label="Title for job outputs"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
19 help="Supply a meaningful name here to remind you what the outputs contain">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
20 <sanitizer invalid_char="">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
21 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
22 </sanitizer>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
23 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
24 <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
25 <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
26 multiple="true" use_header_names="true" size="120" display="checkboxes">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
27 <validator type="no_options" message="Please select at least one column."/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
28 <sanitizer invalid_char="">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
29 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
30 </sanitizer>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
31 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
32 <param name="control_name" type="text" value="Control" size="50" label="Control Name"/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
33 <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
34 multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
35 <validator type="no_options" message="Please select at least one column."/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
36 <sanitizer invalid_char="">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
37 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
38 </sanitizer> <validator type="no_options" message="Please select at least one column."/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
39 <sanitizer invalid_char="">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
40 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
41 </sanitizer>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
42
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
43 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
44 <param name="subjectids" type="text" optional="true" size="120" value = ""
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
45 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"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
46 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'">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
47 <sanitizer>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
48 <valid initial="string.letters,string.digits"><add value="," /> </valid>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
49 </sanitizer>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
50 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
51 <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"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
52 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"/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
53 <param name="useNDF" type="boolean" truevalue="T" falsevalue="F" checked="false" size="1"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
54 label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
55 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"/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
56
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
57 <conditional name="edgeR">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
58 <param name="doedgeR" type="select"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
59 label="Run this model using edgeR"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
60 help="edgeR uses a negative binomial model and seems to be powerful, even with few replicates">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
61 <option value="F">Do not run edgeR</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
62 <option value="T" selected="true">Run edgeR</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
63 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
64 <when value="T">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
65 <param name="edgeR_priordf" type="integer" value="20" size="3"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
66 label="prior.df for tagwise dispersion - lower value = more emphasis on each tag's variance. Replaces prior.n and prior.df = prior.n * residual.df"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
67 help="0 = Use edgeR default. Use a small value to 'smooth' small samples. See edgeR docs and note below"/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
68 </when>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
69 <when value="F"></when>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
70 </conditional>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
71 <conditional name="DESeq2">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
72 <param name="doDESeq2" type="select"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
73 label="Run the same model with DESeq2 and compare findings"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
74 help="DESeq2 is an update to the DESeq package. It uses different assumptions and methods to edgeR">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
75 <option value="F" selected="true">Do not run DESeq2</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
76 <option value="T">Run DESeq2</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
77 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
78 <when value="T">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
79 <param name="DESeq_fitType" type="select">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
80 <option value="parametric" selected="true">Parametric (default) fit for dispersions</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
81 <option value="local">Local fit - this will automagically be used if parametric fit fails</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
82 <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>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
83 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
84 </when>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
85 <when value="F"> </when>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
86 </conditional>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
87 <param name="doVoom" type="select"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
88 label="Run the same model with Voom/limma and compare findings"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
89 help="Voom uses counts per million and a precise transformation of variance so count data can be analysed using limma">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
90 <option value="F" selected="true">Do not run VOOM</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
91 <option value="T">Run VOOM</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
92 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
93 <!--
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
94 <conditional name="camera">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
95 <param name="doCamera" type="select" label="Run the edgeR implementation of Camera GSEA for up/down gene sets"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
96 help="If yes, you can choose a set of genesets to test and/or supply a gmt format geneset collection from your history">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
97 <option value="F" selected="true">Do not run GSEA tests with the Camera algorithm</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
98 <option value="T">Run GSEA tests with the Camera algorithm</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
99 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
100 <when value="T">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
101 <conditional name="gmtSource">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
102 <param name="refgmtSource" type="select"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
103 label="Use a gene set (.gmt) from your history and/or use a built-in (MSigDB etc) gene set">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
104 <option value="indexed" selected="true">Use a built-in gene set</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
105 <option value="history">Use a gene set from my history</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
106 <option value="both">Add a gene set from my history to a built in gene set</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
107 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
108 <when value="indexed">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
109 <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
110 <options from_data_table="gseaGMT_3.1">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
111 <filter type="sort_by" column="2" />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
112 <validator type="no_options" message="No GMT v3.1 files are available - please install them"/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
113 </options>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
114 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
115 </when>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
116 <when value="history">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
117 <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
118 </when>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
119 <when value="both">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
120 <param name="ownGMT" type="data" format="gseagmt" label="Select a Gene Set from your history" />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
121 <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
122 <options from_data_table="gseaGMT_4">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
123 <filter type="sort_by" column="2" />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
124 <validator type="no_options" message="No GMT v4 files are available - please fix tool_data_table and loc files"/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
125 </options>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
126 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
127 </when>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
128 </conditional>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
129 </when>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
130 <when value="F">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
131 </when>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
132 </conditional>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
133 -->
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
134 <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
135 help="Conventional default value of 0.05 recommended"/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
136 <param name="fdrtype" type="select" label="FDR (Type II error) control method"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
137 help="Use fdr or bh typically to control for the number of tests in a reliable way">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
138 <option value="fdr" selected="true">fdr</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
139 <option value="BH">Benjamini Hochberg</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
140 <option value="BY">Benjamini Yukateli</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
141 <option value="bonferroni">Bonferroni</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
142 <option value="hochberg">Hochberg</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
143 <option value="holm">Holm</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
144 <option value="hommel">Hommel</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
145 <option value="none">no control for multiple tests</option>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
146 </param>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
147 </inputs>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
148 <outputs>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
149 <data format="tabular" name="out_edgeR" label="${title}_topTable_edgeR.xls">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
150 <filter>edgeR['doedgeR'] == "T"</filter>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
151 </data>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
152 <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
153 <filter>DESeq2['doDESeq2'] == "T"</filter>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
154 </data>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
155 <data format="tabular" name="out_VOOM" label="${title}_topTable_VOOM.xls">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
156 <filter>doVoom == "T"</filter>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
157 </data>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
158 <data format="html" name="html_file" label="${title}.html"/>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
159 </outputs>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
160 <stdio>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
161 <exit_code range="4" level="fatal" description="Number of subject ids must match total number of samples in the input matrix" />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
162 </stdio>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
163 <tests>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
164 <test>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
165 <param name='input1' value='test_bams2mx.xls' ftype='tabular' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
166 <param name='treatment_name' value='liver' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
167 <param name='title' value='edgeRtest' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
168 <param name='useNDF' value='' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
169 <param name='doedgeR' value='T' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
170 <param name='doVoom' value='T' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
171 <param name='doDESeq2' value='T' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
172 <param name='fdrtype' value='fdr' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
173 <param name='edgeR_priordf' value="8" />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
174 <param name='fdrthresh' value="0.05" />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
175 <param name='control_name' value='heart' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
176 <param name='subjectids' value='' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
177 <param name='Control_cols' value='3,4,5,9' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
178 <param name='Treat_cols' value='2,6,7,8' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
179 <output name='out_edgeR' file='edgeRtest1out.xls' compare='diff' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
180 <output name='html_file' file='edgeRtest1out.html' compare='diff' lines_diff='20' />
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
181 </test>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
182 </tests>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
183
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
184 <configfiles>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
185 <configfile name="runme">
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
186 <![CDATA[
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
187 #
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
188 # edgeR.Rscript
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
189 # updated npv 2011 for R 2.14.0 and edgeR 2.4.0 by ross
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
190 # Performs DGE on a count table containing n replicates of two conditions
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
191 #
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
192 # Parameters
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
193 #
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
194 # 1 - Output Dir
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
195
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
196 # Original edgeR code by: S.Lunke and A.Kaspi
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
197 reallybig = log10(.Machine\$double.xmax)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
198 reallysmall = log10(.Machine\$double.xmin)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
199 library('stringr')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
200 library('gplots')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
201 library('edgeR')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
202 hmap2 = function(cmat,nsamp=100,outpdfname='heatmap2.pdf', TName='Treatment',group=NA,myTitle='title goes here')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
203 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
204 # Perform clustering for significant pvalues after controlling FWER
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
205 samples = colnames(cmat)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
206 gu = unique(group)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
207 gn = rownames(cmat)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
208 if (length(gu) == 2) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
209 col.map = function(g) {if (g==gu[1]) "#FF0000" else "#0000FF"}
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
210 pcols = unlist(lapply(group,col.map))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
211 } else {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
212 colours = rainbow(length(gu),start=0,end=4/6)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
213 pcols = colours[match(group,gu)] }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
214 dm = cmat[(! is.na(gn)),]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
215 # remove unlabelled hm rows
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
216 nprobes = nrow(dm)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
217 # sub = paste('Showing',nprobes,'contigs ranked for evidence of differential abundance')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
218 if (nprobes > nsamp) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
219 dm =dm[1:nsamp,]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
220 #sub = paste('Showing',nsamp,'contigs ranked for evidence for differential abundance out of',nprobes,'total')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
221 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
222 newcolnames = substr(colnames(dm),1,20)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
223 colnames(dm) = newcolnames
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
224 pdf(outpdfname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
225 heatmap.2(dm,main=myTitle,ColSideColors=pcols,col=topo.colors(100),dendrogram="col",key=T,density.info='none',
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
226 Rowv=F,scale='row',trace='none',margins=c(8,8),cexRow=0.4,cexCol=0.5)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
227 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
228 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
229
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
230 hmap = function(cmat,nmeans=4,outpdfname="heatMap.pdf",nsamp=250,TName='Treatment',group=NA,myTitle="Title goes here")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
231 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
232 # for 2 groups only was
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
233 #col.map = function(g) {if (g==TName) "#FF0000" else "#0000FF"}
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
234 #pcols = unlist(lapply(group,col.map))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
235 gu = unique(group)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
236 colours = rainbow(length(gu),start=0.3,end=0.6)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
237 pcols = colours[match(group,gu)]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
238 nrows = nrow(cmat)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
239 mtitle = paste(myTitle,'Heatmap: n contigs =',nrows)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
240 if (nrows > nsamp) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
241 cmat = cmat[c(1:nsamp),]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
242 mtitle = paste('Heatmap: Top ',nsamp,' DE contigs (of ',nrows,')',sep='')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
243 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
244 newcolnames = substr(colnames(cmat),1,20)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
245 colnames(cmat) = newcolnames
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
246 pdf(outpdfname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
247 heatmap(cmat,scale='row',main=mtitle,cexRow=0.3,cexCol=0.4,Rowv=NA,ColSideColors=pcols)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
248 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
249 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
250
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
251 qqPlot = function(descr='qqplot',pvector, outpdf='qqplot.pdf',...)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
252 # stolen from https://gist.github.com/703512
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
253 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
254 o = -log10(sort(pvector,decreasing=F))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
255 e = -log10( 1:length(o)/length(o) )
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
256 o[o==-Inf] = reallysmall
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
257 o[o==Inf] = reallybig
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
258 maint = descr
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
259 pdf(outpdf)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
260 plot(e,o,pch=19,cex=1, main=maint, ...,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
261 xlab=expression(Expected~~-log[10](italic(p))),
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
262 ylab=expression(Observed~~-log[10](italic(p))),
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
263 xlim=c(0,max(e)), ylim=c(0,max(o)))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
264 lines(e,e,col="red")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
265 grid(col = "lightgray", lty = "dotted")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
266 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
267 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
268
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
269 smearPlot = function(DGEList,deTags, outSmear, outMain)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
270 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
271 pdf(outSmear)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
272 plotSmear(DGEList,de.tags=deTags,main=outMain)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
273 grid(col="lightgray", lty="dotted")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
274 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
275 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
276
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
277 boxPlot = function(rawrs,cleanrs,maint,myTitle,pdfname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
278 { #
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
279 nc = ncol(rawrs)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
280 #### for (i in c(1:nc)) {rawrs[(rawrs[,i] < 0),i] = NA}
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
281 fullnames = colnames(rawrs)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
282 newcolnames = substr(colnames(rawrs),1,20)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
283 colnames(rawrs) = newcolnames
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
284 newcolnames = substr(colnames(cleanrs),1,20)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
285 colnames(cleanrs) = newcolnames
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
286 defpar = par(no.readonly=T)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
287 print.noquote('raw contig counts by sample:')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
288 print.noquote(summary(rawrs))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
289 print.noquote('normalised contig counts by sample:')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
290 print.noquote(summary(cleanrs))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
291 pdf(pdfname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
292 par(mfrow=c(1,2))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
293 boxplot(rawrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('Raw:',maint))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
294 grid(col="lightgray",lty="dotted")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
295 boxplot(cleanrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('After ',maint))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
296 grid(col="lightgray",lty="dotted")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
297 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
298 pdfname = "sample_counts_histogram.pdf"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
299 nc = ncol(rawrs)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
300 print.noquote(paste('Using ncol rawrs=',nc))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
301 ncroot = round(sqrt(nc))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
302 if (ncroot*ncroot < nc) { ncroot = ncroot + 1 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
303 m = c()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
304 for (i in c(1:nc)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
305 rhist = hist(rawrs[,i],breaks=100,plot=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
306 m = append(m,max(rhist\$counts))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
307 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
308 ymax = max(m)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
309 ncols = length(fullnames)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
310 if (ncols > 20)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
311 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
312 scale = 7*ncols/20
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
313 pdf(pdfname,width=scale,height=scale)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
314 } else {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
315 pdf(pdfname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
316 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
317 par(mfrow=c(ncroot,ncroot))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
318 for (i in c(1:nc)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
319 hist(rawrs[,i], main=paste("Contig logcount",i), xlab='log raw count', col="maroon",
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
320 breaks=100,sub=fullnames[i],cex=0.8,ylim=c(0,ymax))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
321 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
322 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
323 par(defpar)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
324
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
325 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
326
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
327 cumPlot = function(rawrs,cleanrs,maint,myTitle)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
328 { # updated to use ecdf
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
329 pdfname = "Filtering_rowsum_bar_charts.pdf"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
330 defpar = par(no.readonly=T)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
331 lrs = log(rawrs,10)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
332 lim = max(lrs)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
333 pdf(pdfname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
334 par(mfrow=c(2,1))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
335 hist(lrs,breaks=100,main=paste('Before:',maint),xlab="# Reads (log)",
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
336 ylab="Count",col="maroon",sub=myTitle, xlim=c(0,lim),las=1)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
337 grid(col="lightgray", lty="dotted")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
338 lrs = log(cleanrs,10)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
339 hist(lrs,breaks=100,main=paste('After:',maint),xlab="# Reads (log)",
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
340 ylab="Count",col="maroon",sub=myTitle,xlim=c(0,lim),las=1)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
341 grid(col="lightgray", lty="dotted")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
342 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
343 par(defpar)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
344 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
345
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
346 cumPlot1 = function(rawrs,cleanrs,maint,myTitle)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
347 { # updated to use ecdf
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
348 pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"RowsumCum.pdf",sep='_')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
349 pdf(pdfname)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
350 par(mfrow=c(2,1))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
351 lastx = max(rawrs)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
352 rawe = knots(ecdf(rawrs))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
353 cleane = knots(ecdf(cleanrs))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
354 cy = 1:length(cleane)/length(cleane)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
355 ry = 1:length(rawe)/length(rawe)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
356 plot(rawe,ry,type='l',main=paste('Before',maint),xlab="Log Contig Total Reads",
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
357 ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
358 grid(col="blue")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
359 plot(cleane,cy,type='l',main=paste('After',maint),xlab="Log Contig Total Reads",
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
360 ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
361 grid(col="blue")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
362 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
363 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
364
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
365
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
366
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
367 doGSEA = function(y=NULL,design=NULL,histgmt="",
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
368 bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
369 ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
370 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
371 sink('Camera.log')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
372 genesets = c()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
373 if (bigmt > "")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
374 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
375 bigenesets = readLines(bigmt)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
376 genesets = bigenesets
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
377 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
378 if (histgmt > "")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
379 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
380 hgenesets = readLines(histgmt)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
381 if (bigmt > "") {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
382 genesets = rbind(genesets,hgenesets)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
383 } else {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
384 genesets = hgenesets
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
385 } # use only history if no bi
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
386 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
387 print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
388 genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
389 outf = outfname
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
390 head=paste(myTitle,'edgeR GSEA')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
391 write(head,file=outfname,append=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
392 ntest=length(genesets)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
393 urownames = toupper(rownames(y))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
394 upcam = c()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
395 downcam = c()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
396 for (i in 1:ntest) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
397 gs = unlist(genesets[i])
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
398 g = gs[1] # geneset_id
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
399 u = gs[2]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
400 if (u > "") { u = paste("<a href=\'",u,"\'>",u,"</a>",sep="") }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
401 glist = gs[3:length(gs)] # member gene symbols
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
402 glist = toupper(glist)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
403 inglist = urownames %in% glist
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
404 nin = sum(inglist)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
405 if ((nin > minnin) && (nin < maxnin)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
406 ### print(paste('@@found',sum(inglist),'genes in glist'))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
407 camres = camera(y=y,index=inglist,design=design)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
408 if (! is.null(camres)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
409 rownames(camres) = g # gene set name
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
410 camres = cbind(GeneSet=g,URL=u,camres)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
411 if (camres\$Direction == "Up")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
412 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
413 upcam = rbind(upcam,camres) } else {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
414 downcam = rbind(downcam,camres)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
415 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
416 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
417 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
418 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
419 uscam = upcam[order(upcam\$PValue),]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
420 unadjp = uscam\$PValue
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
421 uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
422 nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
423 dscam = downcam[order(downcam\$PValue),]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
424 unadjp = dscam\$PValue
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
425 dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
426 ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
427 write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
428 write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
429 print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
430 write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
431 print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
432 write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
433 sink()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
434 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
435
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
436
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
437
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
438
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
439 doGSEAatonce = function(y=NULL,design=NULL,histgmt="",
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
440 bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
441 ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
442 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
443 sink('Camera.log')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
444 genesets = c()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
445 if (bigmt > "")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
446 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
447 bigenesets = readLines(bigmt)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
448 genesets = bigenesets
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
449 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
450 if (histgmt > "")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
451 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
452 hgenesets = readLines(histgmt)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
453 if (bigmt > "") {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
454 genesets = rbind(genesets,hgenesets)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
455 } else {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
456 genesets = hgenesets
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
457 } # use only history if no bi
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
458 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
459 print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
460 genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
461 outf = outfname
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
462 head=paste(myTitle,'edgeR GSEA')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
463 write(head,file=outfname,append=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
464 ntest=length(genesets)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
465 urownames = toupper(rownames(y))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
466 upcam = c()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
467 downcam = c()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
468 incam = c()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
469 urls = c()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
470 gsids = c()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
471 for (i in 1:ntest) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
472 gs = unlist(genesets[i])
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
473 gsid = gs[1] # geneset_id
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
474 url = gs[2]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
475 if (url > "") { url = paste("<a href=\'",url,"\'>",url,"</a>",sep="") }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
476 glist = gs[3:length(gs)] # member gene symbols
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
477 glist = toupper(glist)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
478 inglist = urownames %in% glist
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
479 nin = sum(inglist)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
480 if ((nin > minnin) && (nin < maxnin)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
481 incam = c(incam,inglist)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
482 gsids = c(gsids,gsid)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
483 urls = c(urls,url)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
484 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
485 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
486 incam = as.list(incam)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
487 names(incam) = gsids
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
488 allcam = camera(y=y,index=incam,design=design)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
489 allcamres = cbind(geneset=gsids,allcam,URL=urls)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
490 for (i in 1:ntest) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
491 camres = allcamres[i]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
492 res = try(test = (camres\$Direction == "Up"))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
493 if ("try-error" %in% class(res)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
494 cat("test failed, camres = :")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
495 print.noquote(camres)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
496 } else { if (camres\$Direction == "Up")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
497 { upcam = rbind(upcam,camres)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
498 } else { downcam = rbind(downcam,camres)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
499 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
500
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
501 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
502 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
503 uscam = upcam[order(upcam\$PValue),]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
504 unadjp = uscam\$PValue
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
505 uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
506 nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
507 dscam = downcam[order(downcam\$PValue),]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
508 unadjp = dscam\$PValue
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
509 dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
510 ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
511 write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
512 write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
513 print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
514 write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
515 print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
516 write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
517 sink()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
518 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
519
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
520
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
521 edgeIt = function (Count_Matrix=c(),group=c(),out_edgeR=F,out_VOOM=F,out_DESeq2=F,fdrtype='fdr',priordf=5,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
522 fdrthresh=0.05,outputdir='.', myTitle='Differential Counts',libSize=c(),useNDF=F,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
523 filterquantile=0.2, subjects=c(),mydesign=NULL,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
524 doDESeq2=T,doVoom=T,doCamera=T,doedgeR=T,org='hg19',
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
525 histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
526 doCook=F,DESeq_fitType="parameteric")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
527 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
528 # Error handling
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
529 if (length(unique(group))!=2){
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
530 print("Number of conditions identified in experiment does not equal 2")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
531 q()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
532 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
533 require(edgeR)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
534 options(width = 512)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
535 mt = paste(unlist(strsplit(myTitle,'_')),collapse=" ")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
536 allN = nrow(Count_Matrix)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
537 nscut = round(ncol(Count_Matrix)/2)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
538 colTotmillionreads = colSums(Count_Matrix)/1e6
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
539 counts.dataframe = as.data.frame(c())
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
540 rawrs = rowSums(Count_Matrix)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
541 nonzerod = Count_Matrix[(rawrs > 0),] # remove all zero count genes
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
542 nzN = nrow(nonzerod)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
543 nzrs = rowSums(nonzerod)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
544 zN = allN - nzN
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
545 print('# Quantiles for non-zero row counts:',quote=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
546 print(quantile(nzrs,probs=seq(0,1,0.1)),quote=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
547 if (useNDF == T)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
548 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
549 gt1rpin3 = rowSums(Count_Matrix/expandAsMatrix(colTotmillionreads,dim(Count_Matrix)) >= 1) >= nscut
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
550 lo = colSums(Count_Matrix[!gt1rpin3,])
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
551 workCM = Count_Matrix[gt1rpin3,]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
552 cleanrs = rowSums(workCM)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
553 cleanN = length(cleanrs)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
554 meth = paste( "After removing",length(lo),"contigs with fewer than ",nscut," sample read counts >= 1 per million, there are",sep="")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
555 print(paste("Read",allN,"contigs. Removed",zN,"contigs with no reads.",meth,cleanN,"contigs"),quote=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
556 maint = paste('Filter >=1/million reads in >=',nscut,'samples')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
557 } else {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
558 useme = (nzrs > quantile(nzrs,filterquantile))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
559 workCM = nonzerod[useme,]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
560 lo = colSums(nonzerod[!useme,])
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
561 cleanrs = rowSums(workCM)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
562 cleanN = length(cleanrs)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
563 meth = paste("After filtering at count quantile =",filterquantile,", there are",sep="")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
564 print(paste('Read',allN,"contigs. Removed",zN,"with no reads.",meth,cleanN,"contigs"),quote=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
565 maint = paste('Filter below',filterquantile,'quantile')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
566 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
567 cumPlot(rawrs=rawrs,cleanrs=cleanrs,maint=maint,myTitle=myTitle)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
568 allgenes = rownames(workCM)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
569 reg = "^chr([0-9]+):([0-9]+)-([0-9]+)"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
570 genecards="<a href=\'http://www.genecards.org/index.php?path=/Search/keyword/"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
571 ucsc = paste("<a href=\'http://genome.ucsc.edu/cgi-bin/hgTracks?db=",org,sep='')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
572 testreg = str_match(allgenes,reg)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
573 if (sum(!is.na(testreg[,1]))/length(testreg[,1]) > 0.8) # is ucsc style string
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
574 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
575 print("@@ using ucsc substitution for urls")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
576 contigurls = paste0(ucsc,"&amp;position=chr",testreg[,2],":",testreg[,3],"-",testreg[,4],"\'>",allgenes,"</a>")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
577 } else {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
578 print.noquote("@@ using genecards substitution for urls")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
579 contigurls = paste0(genecards,allgenes,"\'>",allgenes,"</a>")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
580 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
581 print(paste("# Total low count contigs per sample = ",paste(lo,collapse=',')),quote=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
582 cmrowsums = rowSums(workCM)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
583 TName=unique(group)[1]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
584 CName=unique(group)[2]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
585 if (is.null(mydesign)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
586 if (length(subjects) == 0)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
587 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
588 mydesign = model.matrix(~group)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
589 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
590 else {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
591 subjf = factor(subjects)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
592 mydesign = model.matrix(~subjf+group) # we block on subject so make group last to simplify finding it
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
593 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
594 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
595 print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=',')))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
596 print.noquote('Using design matrix:')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
597 print.noquote(mydesign)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
598 if (doedgeR) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
599 sink('edgeR.log')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
600 #### Setup DGEList object
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
601 DGEList = DGEList(counts=workCM, group = group)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
602 DGEList = calcNormFactors(DGEList)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
603
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
604 DGEList = estimateGLMCommonDisp(DGEList,mydesign)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
605 comdisp = DGEList\$common.dispersion
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
606 DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
607 if (edgeR_priordf > 0) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
608 print.noquote(paste("prior.df =",edgeR_priordf))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
609 DGEList = estimateGLMTagwiseDisp(DGEList,mydesign,prior.df = edgeR_priordf)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
610 } else {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
611 DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
612 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
613 DGLM = glmFit(DGEList,design=mydesign)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
614 DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
615 efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
616 normData = (1e+06*DGEList\$counts/efflib)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
617 uoutput = cbind(
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
618 Name=as.character(rownames(DGEList\$counts)),
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
619 DE\$table,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
620 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
621 Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums,normData,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
622 DGEList\$counts
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
623 )
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
624 soutput = uoutput[order(DE\$table\$PValue),] # sorted into p value order - for quick toptable
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
625 goodness = gof(DGLM, pcutoff=fdrthresh)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
626 if (sum(goodness\$outlier) > 0) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
627 print.noquote('GLM outliers:')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
628 print(paste(rownames(DGLM)[(goodness\$outlier)],collapse=','),quote=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
629 } else {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
630 print('No GLM fit outlier genes found\n')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
631 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
632 z = limma::zscoreGamma(goodness\$gof.statistic, shape=goodness\$df/2, scale=2)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
633 pdf("edgeR_GoodnessofFit.pdf")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
634 qq = qqnorm(z, panel.first=grid(), main="tagwise dispersion")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
635 abline(0,1,lwd=3)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
636 points(qq\$x[goodness\$outlier],qq\$y[goodness\$outlier], pch=16, col="maroon")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
637 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
638 estpriorn = getPriorN(DGEList)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
639 print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
640 efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
641 normData = (1e+06*DGEList\$counts)/efflib
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
642 lnormData = log(normData + 1e-6,10)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
643 uniqueg = unique(group)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
644 #### Plot MDS
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
645 sample_colors = match(group,levels(group))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
646 sampleTypes = levels(factor(group))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
647 print.noquote(sampleTypes)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
648 pdf("edgeR_MDSplot.pdf")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
649 plotMDS.DGEList(DGEList,main=paste("edgeR MDS for",myTitle),cex=0.5,col=sample_colors,pch=sample_colors)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
650 legend(x="topleft", legend = sampleTypes,col=c(1:length(sampleTypes)), pch=19)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
651 grid(col="blue")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
652 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
653 colnames(normData) = paste( colnames(normData),'N',sep="_")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
654 print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=',')))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
655 nzd = data.frame(log(nonzerod + 1e-2,10))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
656 try( boxPlot(rawrs=nzd,cleanrs=lnormData,maint='TMM Normalisation',myTitle=myTitle,pdfname="edgeR_raw_norm_counts_box.pdf") )
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
657 write.table(soutput,file=out_edgeR, quote=FALSE, sep="\t",row.names=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
658 tt = cbind(
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
659 Name=as.character(rownames(DGEList\$counts)),
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
660 DE\$table,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
661 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
662 Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
663 )
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
664 print.noquote("# edgeR Top tags\n")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
665 tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
666 tt = tt[order(DE\$table\$PValue),]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
667 print.noquote(tt[1:50,])
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
668 deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,])
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
669 nsig = length(deTags)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
670 print(paste('#',nsig,'tags significant at adj p=',fdrthresh),quote=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
671 deColours = ifelse(deTags,'red','black')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
672 pdf("edgeR_BCV_vs_abundance.pdf")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
673 plotBCV(DGEList, cex=0.3, main="Biological CV vs abundance",col.tagwise=deColours)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
674 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
675 dg = DGEList[order(DE\$table\$PValue),]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
676 #normData = (1e+06 * dg\$counts/expandAsMatrix(dg\$samples\$lib.size, dim(dg)))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
677 efflib = dg\$samples\$lib.size*dg\$samples\$norm.factors
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
678 normData = (1e+06*dg\$counts/efflib)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
679 outpdfname="edgeR_top_100_heatmap.pdf"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
680 hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('edgeR Heatmap',myTitle))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
681 outSmear = "edgeR_smearplot.pdf"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
682 outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
683 smearPlot(DGEList=DGEList,deTags=deTags, outSmear=outSmear, outMain = outMain)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
684 qqPlot(descr=paste(myTitle,'edgeR adj p QQ plot'),pvector=tt\$adj.p.value,outpdf='edgeR_qqplot.pdf')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
685 norm.factor = DGEList\$samples\$norm.factors
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
686 topresults.edgeR = soutput[which(soutput\$adj.p.value < fdrthresh), ]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
687 edgeRcountsindex = which(allgenes %in% rownames(topresults.edgeR))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
688 edgeRcounts = rep(0, length(allgenes))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
689 edgeRcounts[edgeRcountsindex] = 1 # Create venn diagram of hits
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
690 sink()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
691 } ### doedgeR
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
692 if (doDESeq2 == T)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
693 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
694 sink("DESeq2.log")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
695 # DESeq2
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
696 require('DESeq2')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
697 library('RColorBrewer')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
698 if (length(subjects) == 0)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
699 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
700 pdata = data.frame(Name=colnames(workCM),Rx=group,row.names=colnames(workCM))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
701 deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ Rx))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
702 } else {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
703 pdata = data.frame(Name=colnames(workCM),Rx=group,subjects=subjects,row.names=colnames(workCM))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
704 deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ subjects + Rx))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
705 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
706 #DESeq2 = DESeq(deSEQds,fitType='local',pAdjustMethod=fdrtype)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
707 #rDESeq = results(DESeq2)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
708 #newCountDataSet(workCM, group)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
709 deSeqDatsizefac = estimateSizeFactors(deSEQds)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
710 deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
711 resDESeq = nbinomWaldTest(deSeqDatdisp, pAdjustMethod=fdrtype)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
712 rDESeq = as.data.frame(results(resDESeq))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
713 rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
714 srDESeq = rDESeq[order(rDESeq\$pvalue),]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
715 write.table(srDESeq,file=out_DESeq2, quote=FALSE, sep="\t",row.names=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
716 qqPlot(descr=paste(myTitle,'DESeq2 adj p qq plot'),pvector=rDESeq\$padj,outpdf='DESeq2_qqplot.pdf')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
717 cat("# DESeq top 50\n")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
718 rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums,URL=contigurls)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
719 srDESeq = rDESeq[order(rDESeq\$pvalue),]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
720 print.noquote(srDESeq[1:50,])
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
721 topresults.DESeq = rDESeq[which(rDESeq\$padj < fdrthresh), ]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
722 DESeqcountsindex = which(allgenes %in% rownames(topresults.DESeq))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
723 DESeqcounts = rep(0, length(allgenes))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
724 DESeqcounts[DESeqcountsindex] = 1
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
725 pdf("DESeq2_dispersion_estimates.pdf")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
726 plotDispEsts(resDESeq)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
727 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
728 ysmall = abs(min(rDESeq\$log2FoldChange))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
729 ybig = abs(max(rDESeq\$log2FoldChange))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
730 ylimit = min(4,ysmall,ybig)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
731 pdf("DESeq2_MA_plot.pdf")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
732 plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
733 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
734 rlogres = rlogTransformation(resDESeq)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
735 sampledists = dist( t( assay(rlogres) ) )
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
736 sdmat = as.matrix(sampledists)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
737 pdf("DESeq2_sample_distance_plot.pdf")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
738 heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"),
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
739 col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
740 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
741 ###outpdfname="DESeq2_top50_heatmap.pdf"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
742 ###hmap2(sresDESeq,nsamp=50,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('DESeq2 vst rlog Heatmap',myTitle))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
743 sink()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
744 result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) )
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
745 if ("try-error" %in% class(result)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
746 print.noquote('DESeq2 plotPCA failed.')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
747 } else {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
748 pdf("DESeq2_PCA_plot.pdf")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
749 #### wtf - print? Seems needed to get this to work
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
750 print(ppca)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
751 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
752 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
753 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
754
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
755 if (doVoom == T) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
756 sink('Voom.log')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
757 if (doedgeR == F) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
758 #### Setup DGEList object
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
759 DGEList = DGEList(counts=workCM, group = group)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
760 DGEList = calcNormFactors(DGEList)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
761 DGEList = estimateGLMCommonDisp(DGEList,mydesign)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
762 DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
763 DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
764 DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
765 norm.factor = DGEList\$samples\$norm.factors
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
766 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
767 pdf("Voom_mean_variance_plot.pdf")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
768 dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
769 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
770 # Use limma to fit data
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
771 fit = lmFit(dat.voomed, mydesign)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
772 fit = eBayes(fit)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
773 rvoom = topTable(fit, coef = length(colnames(mydesign)), adj = fdrtype, n = Inf, sort="none")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
774 qqPlot(descr=paste(myTitle,'Voom-limma adj p QQ plot'),pvector=rvoom\$adj.P.Val,outpdf='Voom_qqplot.pdf')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
775 rownames(rvoom) = rownames(workCM)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
776 rvoom = cbind(rvoom,NReads=cmrowsums)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
777 srvoom = rvoom[order(rvoom\$P.Value),]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
778 write.table(srvoom,file=out_VOOM, quote=FALSE, sep="\t",row.names=F)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
779 rvoom = cbind(rvoom,URL=contigurls)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
780 deTags = rownames(rvoom[rvoom\$adj.p.value < fdrthresh,])
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
781 nsig = length(deTags)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
782 cat("# Voom top 50\n")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
783 print(srvoom[1:50,])
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
784 normData = srvoom\$E
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
785 outpdfname="Voom_top_100_heatmap.pdf"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
786 hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('VOOM Heatmap',myTitle))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
787 outSmear = "Voom_smearplot.pdf"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
788 outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
789 smearPlot(DGEList=rvoom,deTags=deTags, outSmear=outSmear, outMain = outMain)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
790 qqPlot(descr=paste(myTitle,'VOOM adj p QQ plot'),pvector=srvoom\$adj.P.Val,outpdf='Voom_qqplot.pdf')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
791 # Use an FDR cutoff to find interesting samples for edgeR, DESeq and voom/limma
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
792 topresults.voom = rvoom[which(rvoom\$adj.P.Val < fdrthresh), ]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
793 voomcountsindex = which(allgenes %in% topresults.voom\$ID)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
794 voomcounts = rep(0, length(allgenes))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
795 voomcounts[voomcountsindex] = 1
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
796 sink()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
797 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
798
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
799 if (doCamera) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
800 doGSEA(y=DGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
801 outfname=paste(mt,"GSEA.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
802 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
803
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
804 if ((doDESeq2==T) || (doVoom==T) || (doedgeR==T)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
805 if ((doVoom==T) && (doDESeq2==T) && (doedgeR==T)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
806 vennmain = paste(mt,'Voom,edgeR and DESeq2 overlap at FDR=',fdrthresh)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
807 counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
808 VOOM_limma = voomcounts, row.names = allgenes)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
809 } else if ((doDESeq2==T) && (doedgeR==T)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
810 vennmain = paste(mt,'DESeq2 and edgeR overlap at FDR=',fdrthresh)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
811 counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, row.names = allgenes)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
812 } else if ((doVoom==T) && (doedgeR==T)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
813 vennmain = paste(mt,'Voom and edgeR overlap at FDR=',fdrthresh)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
814 counts.dataframe = data.frame(edgeR = edgeRcounts, VOOM_limma = voomcounts, row.names = allgenes)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
815 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
816
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
817 if (nrow(counts.dataframe > 1)) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
818 counts.venn = vennCounts(counts.dataframe)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
819 vennf = "Venn_significant_genes_overlap.pdf"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
820 pdf(vennf)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
821 vennDiagram(counts.venn,main=vennmain,col="maroon")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
822 dev.off()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
823 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
824 } #### doDESeq2 or doVoom
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
825
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
826 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
827 #### Done
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
828
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
829 ###sink(stdout(),append=T,type="message")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
830 builtin_gmt = ""
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
831 history_gmt = ""
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
832 history_gmt_name = ""
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
833 out_edgeR = F
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
834 out_DESeq2 = F
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
835 out_VOOM = "$out_VOOM"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
836 doDESeq2 = $DESeq2.doDESeq2 # make these T or F
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
837 doVoom = $doVoom
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
838 doCamera = F
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
839 doedgeR = $edgeR.doedgeR
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
840 edgeR_priordf = 0
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
841
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
842
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
843 #if $doVoom == "T":
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
844 out_VOOM = "$out_VOOM"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
845 #end if
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
846
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
847 #if $DESeq2.doDESeq2 == "T":
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
848 out_DESeq2 = "$out_DESeq2"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
849 DESeq_fitType = "$DESeq2.DESeq_fitType"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
850 #end if
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
851
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
852 #if $edgeR.doedgeR == "T":
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
853 out_edgeR = "$out_edgeR"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
854 edgeR_priordf = $edgeR.edgeR_priordf
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
855 #end if
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
856
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
857
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
858 if (sum(c(doedgeR,doVoom,doDESeq2)) == 0)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
859 {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
860 write("No methods chosen - nothing to do! Please try again after choosing one or more methods", stderr())
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
861 quit(save="no",status=2)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
862 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
863
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
864 Out_Dir = "$html_file.files_path"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
865 Input = "$input1"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
866 TreatmentName = "$treatment_name"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
867 TreatmentCols = "$Treat_cols"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
868 ControlName = "$control_name"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
869 ControlCols= "$Control_cols"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
870 org = "$input1.dbkey"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
871 if (org == "") { org = "hg19"}
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
872 fdrtype = "$fdrtype"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
873 fdrthresh = $fdrthresh
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
874 useNDF = $useNDF
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
875 fQ = $fQ # non-differential centile cutoff
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
876 myTitle = "$title"
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
877 sids = strsplit("$subjectids",',')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
878 subjects = unlist(sids)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
879 nsubj = length(subjects)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
880 TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
881 CCols = as.numeric(strsplit(ControlCols,",")[[1]])-1
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
882 cat('Got TCols=')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
883 cat(TCols)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
884 cat('; CCols=')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
885 cat(CCols)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
886 cat('\n')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
887 useCols = c(TCols,CCols)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
888 if (file.exists(Out_Dir) == F) dir.create(Out_Dir)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
889 Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t') #Load tab file assume header
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
890 snames = colnames(Count_Matrix)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
891 nsamples = length(snames)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
892 if (nsubj > 0 & nsubj != nsamples) {
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
893 options("show.error.messages"=T)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
894 mess = paste('Fatal error: Supplied subject id list',paste(subjects,collapse=','),
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
895 'has length',nsubj,'but there are',nsamples,'samples',paste(snames,collapse=','))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
896 write(mess, stderr())
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
897 quit(save="no",status=4)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
898 }
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
899 if (length(subjects) != 0) {subjects = subjects[useCols]}
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
900 Count_Matrix = Count_Matrix[,useCols] ### reorder columns
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
901 rn = rownames(Count_Matrix)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
902 islib = rn %in% c('librarySize','NotInBedRegions')
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
903 LibSizes = Count_Matrix[subset(rn,islib),][1] # take first
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
904 Count_Matrix = Count_Matrix[subset(rn,! islib),]
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
905 group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) ) #Build a group descriptor
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
906 group = factor(group, levels=c(ControlName,TreatmentName))
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
907 colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_") #Relable columns
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
908 results = edgeIt(Count_Matrix=Count_Matrix,group=group, out_edgeR=out_edgeR, out_VOOM=out_VOOM, out_DESeq2=out_DESeq2,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
909 fdrtype='BH',mydesign=NULL,priordf=edgeR_priordf,fdrthresh=fdrthresh,outputdir='.',
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
910 myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=subjects,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
911 doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
912 histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
913 sessionInfo()
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
914 ]]>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
915 </configfile>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
916 </configfiles>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
917 <help>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
918
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
919 **What it does**
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
920
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
921 Allows short read sequence counts from controlled experiments to be analysed for differentially expressed genes.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
922 Optionally adds a term for subject if not all samples are independent or if some other factor needs to be blocked in the design.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
923
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
924 **Input**
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
925
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
926 Requires a count matrix as a tabular file. These are best made using the companion HTSeq_ based counter Galaxy wrapper
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
927 and your fave gene model to generate inputs. Each row is a genomic feature (gene or exon eg) and each column the
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
928 non-negative integer count of reads from one sample overlapping the feature.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
929 The matrix must have a header row uniquely identifying the source samples, and unique row names in
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
930 the first column. Typically the row names are gene symbols or probe ids for downstream use in GSEA and other methods.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
931
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
932 **Specifying comparisons**
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
933
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
934 This is basically dumbed down for two factors - case vs control.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
935
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
936 More complex interfaces are possible but painful at present.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
937 Probably need to specify a phenotype file to do this better.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
938 Work in progress. Send code.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
939
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
940 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),
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
941 put a comma separated list of indicators for every sample (whether modelled or not!) indicating (eg) the subject number or
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
942 A list of integers, one for each subject or an empty string if samples are all independent.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
943 If not empty, there must be exactly as many integers in the supplied integer list as there are columns (samples) in the count matrix.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
944 Integers for samples that are not in the analysis *must* be present in the string as filler even if not used.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
945
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
946 So if you have 2 pairs out of 6 samples, you need to put in unique integers for the unpaired ones
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
947 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
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
948 8,9,1,1,2,2
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
949 as subject IDs to indicate two paired samples from the same subject in columns 3/4 and 5/6
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
950
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
951 **Methods available**
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
952
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
953 You can run 3 popular Bioconductor packages available for count data.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
954
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
955 edgeR - see edgeR_ for details
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
956
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
957 VOOM/limma - see limma_VOOM_ for details
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
958
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
959 DESeq2 - see DESeq2_ for details
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
960
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
961 and optionally camera in edgeR which works better if MSigDB is installed.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
962
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
963 **Outputs**
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
964
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
965 Some helpful plots and analysis results. Note that most of these are produced using R code
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
966 suggested by the excellent documentation and vignettes for the Bioconductor
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
967 packages invoked. The Tool Factory is used to automatically lay these out for you to enjoy.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
968
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
969 **Note on Voom**
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
970
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
971 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.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
972
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
973 This function is intended to process RNA-Seq or ChIP-Seq data prior to linear modelling in limma.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
974
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
975 voom is an acronym for mean-variance modelling at the observational level.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
976 The key concern is to estimate the mean-variance relationship in the data, then use this to compute appropriate weights for each observation.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
977 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.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
978 This function estimates the mean-variance trend for log-counts, then assigns a weight to each observation based on its predicted variance.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
979 The weights are then used in the linear modelling process to adjust for heteroscedasticity.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
980
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
981 In an experiment, a count value is observed for each tag in each sample. A tag-wise mean-variance trend is computed using lowess.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
982 The tag-wise mean is the mean log2 count with an offset of 0.5, across samples for a given tag.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
983 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.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
984 Tags with zero counts across all samples are not included in the lowess fit. Optional normalization is performed using normalizeBetweenArrays.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
985 Using fitted values of log2 counts from a linear model fit by lmFit, variances from the mean-variance trend were interpolated for each observation.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
986 This was carried out by approxfun. Inverse variance weights can be used to correct for mean-variance trend in the count data.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
987
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
988
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
989 Author(s)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
990
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
991 Charity Law and Gordon Smyth
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
992
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
993 References
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
994
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
995 Law, CW (2013). Precision weights for gene expression analysis. PhD Thesis. University of Melbourne, Australia.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
996
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
997 Law, CW, Chen, Y, Shi, W, Smyth, GK (2013). Voom! Precision weights unlock linear model analysis tools for RNA-seq read counts.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
998 Technical Report 1 May 2013, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Reseach, Melbourne, Australia.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
999 http://www.statsci.org/smyth/pubs/VoomPreprint.pdf
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1000
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1001 See Also
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1002
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1003 A voom case study is given in the edgeR User's Guide.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1004
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1005 vooma is a similar function but for microarrays instead of RNA-seq.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1006
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1007
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1008 ***old rant on changes to Bioconductor package variable names between versions***
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1009
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1010 The edgeR authors made a small cosmetic change in the name of one important variable (from p.value to PValue)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1011 breaking this and all other code that assumed the old name for this variable,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1012 between edgeR2.4.4 and 2.4.6 (the version for R 2.14 as at the time of writing).
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1013 This means that all code using edgeR is sensitive to the version. I think this was a very unwise thing
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1014 to do because it wasted hours of my time to track down and will similarly cost other edgeR users dearly
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1015 when their old scripts break. This tool currently now works with 2.4.6.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1016
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1017 **Note on prior.N**
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1018
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1019 http://seqanswers.com/forums/showthread.php?t=5591 says:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1020
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1021 *prior.n*
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1022
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1023 The value for prior.n determines the amount of smoothing of tagwise dispersions towards the common dispersion.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1024 You can think of it as like a "weight" for the common value. (It is actually the weight for the common likelihood
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1025 in the weighted likelihood equation). The larger the value for prior.n, the more smoothing, i.e. the closer your
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1026 tagwise dispersion estimates will be to the common dispersion. If you use a prior.n of 1, then that gives the
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1027 common likelihood the weight of one observation.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1028
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1029 In answer to your question, it is a good thing to squeeze the tagwise dispersions towards a common value,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1030 or else you will be using very unreliable estimates of the dispersion. I would not recommend using the value that
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1031 you obtained from estimateSmoothing()---this is far too small and would result in virtually no moderation
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1032 (squeezing) of the tagwise dispersions. How many samples do you have in your experiment?
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1033 What is the experimental design? If you have few samples (less than 6) then I would suggest a prior.n of at least 10.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1034 If you have more samples, then the tagwise dispersion estimates will be more reliable,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1035 so you could consider using a smaller prior.n, although I would hesitate to use a prior.n less than 5.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1036
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1037
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1038 From Bioconductor Digest, Vol 118, Issue 5, Gordon writes:
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1039
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1040 Dear Dorota,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1041
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1042 The important settings are prior.df and trend.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1043
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1044 prior.n and prior.df are related through prior.df = prior.n * residual.df,
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1045 and your experiment has residual.df = 36 - 12 = 24. So the old setting of
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1046 prior.n=10 is equivalent for your data to prior.df = 240, a very large
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1047 value. Going the other way, the new setting of prior.df=10 is equivalent
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1048 to prior.n=10/24.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1049
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1050 To recover old results with the current software you would use
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1051
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1052 estimateTagwiseDisp(object, prior.df=240, trend="none")
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1053
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1054 To get the new default from old software you would use
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1055
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1056 estimateTagwiseDisp(object, prior.n=10/24, trend=TRUE)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1057
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1058 Actually the old trend method is equivalent to trend="loess" in the new
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1059 software. You should use plotBCV(object) to see whether a trend is
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1060 required.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1061
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1062 Note you could also use
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1063
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1064 prior.n = getPriorN(object, prior.df=10)
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1065
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1066 to map between prior.df and prior.n.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1067
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1068 ----
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1069
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1070 **Attributions**
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1071
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1072 edgeR - edgeR_
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1073
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1074 VOOM/limma - limma_VOOM_
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1075
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1076 DESeq2 - DESeq2_ for details
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1077
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1078 See above for Bioconductor package documentation for packages exposed in Galaxy by this tool and app store package.
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1079
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1080 Galaxy_ (that's what you are using right now!) for gluing everything together
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1081
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1082 Otherwise, all code and documentation comprising this tool was written by Ross Lazarus and is
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1083 licensed to you under the LGPL_ like other rgenetics artefacts
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1084
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1085 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1086 .. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1087 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1088 .. _DESeq2: http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1089 .. _limma_VOOM: http://www.bioconductor.org/packages/release/bioc/html/limma.html
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1090 .. _Galaxy: http://getgalaxy.org
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1091 </help>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1092
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1093 </tool>
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1094
60aceade5350 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
fubar
parents:
diff changeset
1095