Mercurial > repos > erasmus-medical-center > voom_transform

diff voom_transform.R @ 0:c6a3a93a237e draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
author erasmus-medical-center
date Wed, 25 Jan 2017 10:13:10 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/voom_transform.R	Wed Jan 25 10:13:10 2017 -0500
@@ -0,0 +1,18 @@
+#!/usr/bin/env Rscript
+
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+library("getopt")
+library("limma")
+
+spec <- matrix(c( 
+    "expressionmatrix", "e", 1, "character",
+    "transformedmatrix", "t", 1, "character"
+    ), byrow=TRUE, ncol=4)
+opt <- getopt(spec)
+
+em <-  read.delim(opt$expressionmatrix,header=T,row.names=1,stringsAsFactors=F,check.names=FALSE,na.strings=c(""))
+
+vem <- voom(em)
+write.table(file=opt$transformedmatrix,vem$E,sep="\t",row.names=TRUE,col.names=NA,quote=F)