Mercurial > repos > davidecangelosi > pipe_t
changeset 19:8503457bd0c4 draft
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit f98eba79c2036aa3e1b8f9048c0b1e61d4d87b60
| author | davidecangelosi |
|---|---|
| date | Tue, 28 May 2019 04:35:18 -0400 |
| parents | 2a6088c11d42 |
| children | 9227f7b1c50b |
| files | pipe-t.R |
| diffstat | 1 files changed, 1 insertions(+), 9 deletions(-) [+] |
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--- a/pipe-t.R Tue May 28 04:33:16 2019 -0400 +++ b/pipe-t.R Tue May 28 04:35:18 2019 -0400 @@ -885,14 +885,6 @@ stop("Enter something that switches me!") ) -if (DEAMethod=="ttest") { - #Differential expression analysis (paired t test+BH). Returns Fold change in linear scale. - DEG<-ttestCtData(qFiltNAs, groups = files$Treatment, alternative = alternative, paired = ifelse(paired=="TRUE", TRUE, FALSE), replicates =ifelse(replicates=="TRUE", TRUE, FALSE), sort=ifelse(sort=="TRUE", TRUE, FALSE), stringent=ifelse(stringent=="TRUE", TRUE, FALSE), p.adjust=padjust) - write.table(DEG, file=outputDEA, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") -} -if (DEAMethod=="rp") { - DEG<-RP(exprs(qFiltNAs), as.numeric(pData(qFiltNAs)$Treatment)-1, num.perm = 1000,logged = TRUE, gene.names = featureNames(qFiltNAs), huge=TRUE, plot = FALSE, rand = 123) - write.table(DEG[1:5], file=outputDEA, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") -} + cat("\n Differential expression analysis completed correctly! \n") cat("\n Workflow ended correctly! \n")