Mercurial > repos > bgruening > deseq2
changeset 26:bac4ebab1122 draft
Uploaded
author | bgruening |
---|---|
date | Wed, 26 Nov 2014 12:06:14 -0500 |
parents | 2f52c1a27205 |
children | 05a4f4e317a0 |
files | deseq2.R |
diffstat | 1 files changed, 7 insertions(+), 2 deletions(-) [+] |
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--- a/deseq2.R Wed Nov 26 11:14:42 2014 -0500 +++ b/deseq2.R Wed Nov 26 12:06:14 2014 -0500 @@ -49,7 +49,6 @@ select <- order(rowMeans(counts(dds,normalized=TRUE)),decreasing=TRUE)[1:30] hmcol <- colorRampPalette(brewer.pal(9, "GnBu"))(100) - rld <- rlogTransformation(dds, blind=TRUE) vsd <- varianceStabilizingTransformation(dds, blind=TRUE) distsRL <- dist(t(assay(rld))) @@ -63,6 +62,7 @@ sampleTable<-data.frame() factorNames<-c() +primaryfactor = TRUE for(factor in factorsList){ factorName<-factor[[1]] factorNames<-append(factorNames, factorName) @@ -70,14 +70,19 @@ c = length(factorValuesMapList) for (factorValuesMap in factorValuesMapList){ for(files in factorValuesMap){ + fvc = 0 for(file in files){ - sampleTable[basename(file),"sampleName"]<-file + fvc = fvc+1 + if(primaryfactor) { + sampleTable[basename(file),"sampleName"]<-paste(fvc,names(factorValuesMap),sep="_") + } sampleTable[basename(file),"fileName"]<-file sampleTable[basename(file),factorName]<-paste(c,names(factorValuesMap),sep="_") } } c = c-1 } + primaryfactor = FALSE } factorNames<-rev(factorNames)