Mercurial > repos > iuc > limma_voom

diff limma_voom.R @ 16:f564807836a9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 349e35a66009449851b21e2810bc5aaa58225fca
author iuc
date Sat, 09 Feb 2019 07:34:33 -0500
parents 94f82c79fa66
children 4bd4353bfe5f
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--- a/limma_voom.R	Sat Jan 05 05:35:00 2019 -0500
+++ b/limma_voom.R	Sat Feb 09 07:34:33 2019 -0500
@@ -837,9 +837,9 @@
 
     # Write top expressions table
     if (wantTreat) {
-        top <- topTreat(fit, coef=i, number=Inf, sort.by="P")
+        top <- topTreat(fit, coef=i, adjust.method=opt$pAdjOpt, number=Inf, sort.by="P")
     } else{
-        top <- topTable(fit, coef=i, number=Inf, sort.by="P")
+        top <- topTable(fit, coef=i, adjust.method=opt$pAdjOpt, number=Inf, sort.by="P")
     }
     write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE)
     linkName <- paste0(deMethod, "_", con, ".tsv")