Mercurial > repos > sblanck > smagexp
changeset 11:f9732f6bf218 draft
planemo upload commit 3cad4bb49300f86625d62d40ea7e2ea2ba40e314-dirty
| author | sblanck |
|---|---|
| date | Thu, 11 May 2017 10:20:35 -0400 |
| parents | 56267e3293b2 |
| children | 2da91c541ae4 |
| files | Analyse.R Analyse.xml |
| diffstat | 2 files changed, 10 insertions(+), 7 deletions(-) [+] |
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--- a/Analyse.R Thu May 11 08:31:34 2017 -0400 +++ b/Analyse.R Thu May 11 10:20:35 2017 -0400 @@ -20,7 +20,8 @@ make_option("--htmloutput",type="character",default=NULL,help="Output html report"), make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"), make_option("--tabularoutput",type="character",default=NULL,help="Output text file"), - make_option("--htmltemplate",type="character",default=NULL,help="html template)") + make_option("--htmltemplate",type="character",default=NULL,help="html template)"), + make_option("--tooldirectory",type="character",default=NULL,help="tool directory)") ); @@ -62,6 +63,7 @@ result.path=opt$htmloutputpath result.tabular=opt$tabularoutput result.template=opt$htmltemplate +tooldirectory=opt$tooldirectory #file.copy(targetFile,"./targetFile.txt") @@ -102,18 +104,17 @@ f <- as.factor(condNames) #eset$description <- factors design <- model.matrix(~ 0+f) -design colnames(design) <- levels(f) -colnames(design) +#colnames(design) fit <- lmFit(eset, design) -fit + #cont.matrix <- makeContrasts(C1=paste0(condition1Name,"-",condition2Name), levels=design) cont.matrix <- makeContrasts(G0-G1, levels=design) -cont.matrix +#cont.matrix fit2 <- contrasts.fit(fit, cont.matrix) fit2 <- eBayes(fit2) -fit2 + tT <- topTable(fit2, adjust="fdr", sort.by="B", number=nbresult) #head(exprs(eset)) @@ -121,7 +122,8 @@ gpl <- annotation(eset) if (substr(x = gpl,1,3)!="GPL"){ #if the annotation info does not start with "GPL" we retrieve the corresponding GPL annotation - mapping=read.csv("gplToBioc.csv",stringsAsFactors=FALSE) + print(getwd()) + mapping=read.csv(paste0(tooldirectory,"/gplToBioc.csv"),stringsAsFactors=FALSE) gpl=mapping[which(mapping$bioc_package==annotation(eset)),]$gpl gpl=gpl[1]