Mercurial > repos > bgruening > deseq2
changeset 24:1261539a93e9 draft
Uploaded
| author | bgruening |
|---|---|
| date | Wed, 26 Nov 2014 04:51:23 -0500 |
| parents | f8a59b35c397 |
| children | 2f52c1a27205 |
| files | deseq2.R deseq2.xml test-data/GSM461176_untreat_single.counts test-data/GSM461177_untreat_paired.counts test-data/GSM461178_untreat_paired.counts test-data/GSM461179_treat_single.counts test-data/GSM461180_treat_paired.counts test-data/GSM461181_treat_paired.counts test-data/GSM461182_untreat_single.counts tool_dependencies.xml |
| diffstat | 10 files changed, 104146 insertions(+), 5 deletions(-) [+] |
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--- a/deseq2.R Sat Nov 15 06:18:50 2014 -0500 +++ b/deseq2.R Wed Nov 26 04:51:23 2014 -0500 @@ -6,6 +6,9 @@ library('getopt') library('rjson') library('DESeq2') +library("RColorBrewer") +library("gplots") + options(stringAsfactors = FALSE, useFancyQuotes = FALSE) args <- commandArgs(trailingOnly = TRUE) @@ -44,8 +47,6 @@ plotDispEsts(dds, main= paste(title_prefix, "Dispersion estimate plot")) plotMA(dds, main= paste(title_prefix, "MA-plot")) - library("RColorBrewer") - library("gplots") select <- order(rowMeans(counts(dds,normalized=TRUE)),decreasing=TRUE)[1:30] hmcol <- colorRampPalette(brewer.pal(9, "GnBu"))(100) @@ -91,7 +92,7 @@ design = designFormula) ddsHTSeq <- DESeq(ddsHTSeq) -ddsHTSeq <- nbinomWaldTest(ddsHTSeq, cooksCutoff=FALSE) +#ddsHTSeq <- nbinomWaldTest(ddsHTSeq, cooksCutoff=FALSE) ddsHTSeq deseqRes <- results(ddsHTSeq) mcols(deseqRes)$description @@ -115,7 +116,7 @@ ddsHTSeqFilt <- ddsHTSeq[use, ] ddsHTSeqFilt <- DESeq(ddsHTSeqFilt) -ddsHTSeqFilt <- nbinomWaldTest(ddsHTSeqFilt, cooksCutoff=FALSE) +#ddsHTSeqFilt <- nbinomWaldTest(ddsHTSeqFilt, cooksCutoff=FALSE) ddsHTSeqFilt deseqResFilt <- results(ddsHTSeqFilt) mcols(deseqResFilt)$description
--- a/deseq2.xml Sat Nov 15 06:18:50 2014 -0500 +++ b/deseq2.xml Wed Nov 26 04:51:23 2014 -0500 @@ -3,6 +3,7 @@ <requirements> <requirement type="binary">Rscript</requirement> <requirement type="R-module">DESeq2</requirement> + <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> <requirement type="package" version="3.1.0">R</requirement> <requirement type="package" version="1.6.1">deseq2</requirement> </requirements> @@ -90,6 +91,24 @@ </data> </outputs> + <tests> + <test> + <param name="factorName" value="Treatment"/> + <param name="factorLevel" value="Treated"/> + <param name="countsFile" value="GSM461179_treat_single.counts"/> + <param name="countsFile" value="GSM461180_treat_paired.counts"/> + <param name="countsFile" value="GSM461181_treat_paired.counts"/> + <param name="factorLevel" value="Untreated"/> + <param name="countsFile" value="GSM461176_untreat_single.counts"/> + <param name="countsFile" value="GSM461177_untreat_paired.counts"/> + <param name="countsFile" value="GSM461178_untreat_paired.counts"/> + <param name="countsFile" value="GSM461182_untreat_single.counts"/> + <output name="deseq_out" file="deseq2_out.txt"/> + <output name="deseq_out_filtered" file="deseq_out_filtered.txt"/> + <output name="plots" file="deseq_plots.pdf"/> + </test> + </tests> + <help> .. class:: infomark
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--- a/tool_dependencies.xml Sat Nov 15 06:18:50 2014 -0500 +++ b/tool_dependencies.xml Wed Nov 26 04:51:23 2014 -0500 @@ -1,6 +1,9 @@ <?xml version="1.0"?> <tool_dependency> + <package name="R" version="3.1.0"> + <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> <package name="deseq2" version="1.6.1"> - <repository changeset_revision="feb1e4cb43f3" name="package_deseq2_1_6_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="5beee6b62be7" name="package_deseq2_1_6_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>