# HG changeset patch # User bgruening # Date 1416995483 18000 # Node ID 1261539a93e92ccede00e93eacecfb4ebc2b73f8 # Parent f8a59b35c3975c400831806b778902b868c4b8dc Uploaded diff -r f8a59b35c397 -r 1261539a93e9 deseq2.R --- 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 diff -r f8a59b35c397 -r 1261539a93e9 deseq2.xml --- 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 @@ Rscript DESeq2 + R deseq2 @@ -90,6 +91,24 @@ + + + + + + + + + + + + + + + + + + .. class:: infomark diff -r f8a59b35c397 -r 1261539a93e9 test-data/GSM461176_untreat_single.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461176_untreat_single.counts Wed Nov 26 04:51:23 2014 -0500 @@ -0,0 +1,14874 @@ +FBgn0000003 0 +FBgn0000008 15 +FBgn0000014 0 +FBgn0000015 0 +FBgn0000017 1227 +FBgn0000018 92 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+ambiguous 48373 +too_low_aQual 0 +not_aligned 0 +alignment_not_unique 6896814 diff -r f8a59b35c397 -r 1261539a93e9 tool_dependencies.xml --- 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 @@ + + + - +