Mercurial > repos > erasmus-medical-center > voom_transform
comparison voom_transform.R @ 0:c6a3a93a237e draft default tip
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 |
| parents | |
| children |
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| -1:000000000000 | 0:c6a3a93a237e |
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| 1 #!/usr/bin/env Rscript | |
| 2 | |
| 3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
| 4 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | |
| 5 | |
| 6 library("getopt") | |
| 7 library("limma") | |
| 8 | |
| 9 spec <- matrix(c( | |
| 10 "expressionmatrix", "e", 1, "character", | |
| 11 "transformedmatrix", "t", 1, "character" | |
| 12 ), byrow=TRUE, ncol=4) | |
| 13 opt <- getopt(spec) | |
| 14 | |
| 15 em <- read.delim(opt$expressionmatrix,header=T,row.names=1,stringsAsFactors=F,check.names=FALSE,na.strings=c("")) | |
| 16 | |
| 17 vem <- voom(em) | |
| 18 write.table(file=opt$transformedmatrix,vem$E,sep="\t",row.names=TRUE,col.names=NA,quote=F) |