Commits (1)
......@@ -118,8 +118,11 @@ for (i in 1:a) {
###################### Run EdgeR ########################
###################### Run QuSage ######################
MSIG.geneSets <- read.gmt('geneset.gmt')
run.qusage <- 0
if (file.exists('geneset.gmt')) {
MSIG.geneSets <- read.gmt('geneset.gmt')
run.qusage <- 1
}
design <- model.matrix(~grps)
d <- DGEList(counts=countTable,group=grps,lib.size=libSizes)
......@@ -166,10 +169,12 @@ for (i in 1:a) {
heatmap.2(zscores2, col = bluered(100),Rowv = as.dendrogram(STREE), RowSideColors = col.blocks,dendrogram='row', cexCol=textscale,labCol=s$symbol,srtRow=45,srtCol=45,trace="none", margins=c(5, 5))
legend("topright",legend=grpnames,col=rainbow(length(grpnames)),pch=20,cex=0.5)
dev.off()
gcont <- paste(cond[j],cond[i],sep='-')
qs.results = qusage(logcpm, grps,gcont,MSIG.geneSets)
save(qs.results,file=paste(cond[i],'_',cond[j],'.qusage.rda',sep=""))
}
if (run.qusage > 0) {
gcont <- paste(cond[j],cond[i],sep='-')
qs.results = qusage(logcpm, grps,gcont,MSIG.geneSets)
save(qs.results,file=paste(cond[i],'_',cond[j],'.qusage.rda',sep=""))
}
}
}
}
}
......
......@@ -41,5 +41,8 @@ else
module load R/3.2.1-intel
Rscript $baseDir/dea.R
Rscript $baseDir/build_ballgown.R *_stringtie
perl $baseDir/concat_edgeR.pl *.edgeR.txt
if [[ -n `ls *.edgeR.txt` ]]
then
perl $baseDir/concat_edgeR.pl *.edgeR.txt
fi
fi