Fix local FDR, Now you can use it

DGE-Seq_Analyzer.R

@@ -245,11 +245,11 @@ FDR.res<-list()
 for(comp in comps){
   DE[[comp]]<-data.frame(res[[comp]])
   rownames(DE[[comp]])<-genes
-  FDR.res[[comp]]<-fdrtool(res[[comp]]$stat[which(!is.na(res[[comp]]$stat))], statistic= "normal", plot = F)
+  FDR.res[[comp]]<-fdrtool(res[[comp]]$pvalue[which(!is.na(res[[comp]]$pvalue))], statistic= "normal", plot = F)
   for(item in c("pval","qval","lfdr")){
     stat<-FDR.res[[comp]][[item]]
     FDR.res[[comp]][[item]]<-rep(NA,length(genes))
-    FDR.res[[comp]][[item]][which(!is.na(res[[comp]]$stat))]<-stat
+    FDR.res[[comp]][[item]][which(!is.na(res[[comp]]$pvalue))]<-stat
   }
   DE[[comp]]$localFDR<-FDR.res[[comp]]$qval
 }

functions/RNASeq.R

@@ -678,13 +678,11 @@ getDBterms<-function(geneSym,geneEntrez=NULL, corrIdGenes=NULL, speciesData=NULL
 	}
 }
 
-exportEnrich<-function(enrichResults,file,quote = FALSE,sep = "\t",col.names = TRUE,row.names = FALSE,geneCol="leadingEdge",...){
-	enrichResults$Gene<-sapply(enrichResults[[geneCol]],function(x){ return(paste0(x,collapse=sep))})
-	enrichResults[[geneCol]]<-NULL
-	write.table(enrichResults,file,quote = quote,sep = sep,col.names = col.names,row.names = row.names,...)
+exportEnrich<-function(enrichResults,file,quote = FALSE,sep ="\t",col.names = TRUE,row.names = FALSE,geneCol="leadingEdge",...){
+  enrichResults[[geneCol]]<-sapply(enrichResults[[geneCol]],function(x) paste0(x,collapse=sep))
+  write.table(enrichResults,file,quote = quote,sep = sep,col.names = col.names,row.names = row.names,...)
 }
 
-
 calConsensusRankingOld<-function(genes,pvalues,logFoldChanges){
 	pvalues <- 1-pvalues; abslogFoldChanges<-abs(logFoldChanges)
 	dataRank<-data.frame(pval=pvalues,LFC=abslogFoldChanges,row.names=genes)