# HG changeset patch
# User davidecangelosi
# Date 1559032518 14400
# Node ID 8503457bd0c4bb6076205cafb4c0a6cc82b486bf
# Parent  2a6088c11d42db4d295d0bcc70b52a222b517942
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit f98eba79c2036aa3e1b8f9048c0b1e61d4d87b60

diff -r 2a6088c11d42 -r 8503457bd0c4 pipe-t.R
--- 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")