changed output format to contain FPKM etc. ; fixed a bug for paired-end reads

[rsem.git] / EBSeq / R / QQP.R

diff --git a/EBSeq/R/QQP.R b/EBSeq/R/QQP.R
deleted file mode 100644 (file)
index 686aa92..0000000
--- a/EBSeq/R/QQP.R
+++ /dev/null
@@ -1,14 +0,0 @@
-QQP <-
-function(QList,AlphaResult,BetaResult,name,AList="F",GroupName){
-       
-                   for (i in 1:length(BetaResult)){
-                               tmpSize=length(QList[[i]][QList[[i]]<1 & !is.na(QList[[i]])])
-                       if (AList=="F") rdpts=rbeta(tmpSize,AlphaResult,BetaResult[i])
-                               else rdpts=rbeta(tmpSize,AlphaResult[i],BetaResult[i])
-       qqplot(QList[[i]][QList[[i]]<1], rdpts,xlab="estimated q's", ylab="simulated q's from fitted beta",main=paste(name,GroupName[i],sep=" "),xlim=c(0,1),ylim=c(0,1))
-       fit=lm(sort(rdpts)~sort(QList[[i]][QList[[i]]<1  & !is.na(QList[[i]])]))
-       abline(fit,col="red")
-       
-                       }
-}
-