Mercurial > repos > iuc > edger

diff edger.R @ 6:555659de7321 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629
author iuc
date Sat, 09 Feb 2019 07:20:20 -0500
parents fb9b9f0f2f06
children 3d89af8a44f0
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--- a/edger.R	Tue Feb 05 20:57:30 2019 -0500
+++ b/edger.R	Sat Feb 09 07:20:20 2019 -0500
@@ -526,7 +526,7 @@
     flatCount[i] <- sumStatus["NotSig", ]
                                              
     # Write top expressions table
-    top <- topTags(res, n=Inf, sort.by="PValue")
+    top <- topTags(res, adjust.method=opt$pAdjOpt, n=Inf, sort.by="PValue")
     write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE)
     
     linkName <- paste0("edgeR_", contrastData[i], ".tsv")