From 0eb2c5f6c93f59d8298626714df5ac308186466d Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 22 May 2020 14:03:50 -0500
Subject: [PATCH] update statanal in RNASEq to skip ifno edgeR out
---
genect_rnaseq/dea.R | 17 +++++++++++------
genect_rnaseq/statanal.sh | 5 ++++-
2 files changed, 15 insertions(+), 7 deletions(-)
diff --git a/genect_rnaseq/dea.R b/genect_rnaseq/dea.R
index d2509a9..4cd7419 100755
--- a/genect_rnaseq/dea.R
+++ b/genect_rnaseq/dea.R
@@ -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=""))
+ }
+ }
}
}
}
diff --git a/genect_rnaseq/statanal.sh b/genect_rnaseq/statanal.sh
index 9cba1e3..fd36f0f 100644
--- a/genect_rnaseq/statanal.sh
+++ b/genect_rnaseq/statanal.sh
@@ -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
--
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