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

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

diff --git a/EBSeq/R/TPFDRplot.R b/EBSeq/R/TPFDRplot.R
deleted file mode 100644 (file)
index 9304330..0000000
--- a/EBSeq/R/TPFDRplot.R
+++ /dev/null
@@ -1,39 +0,0 @@
-TPFDRplot <-
-function(DESeqP, EBZ, TrueDE, main, FDR=NULL){
-       Seq=seq(0.001,0.5,by=0.001)
-       DETPR=rep(0,length(Seq))
-       EBTPR=rep(0,length(Seq))
-       DEFDR=rep(0,length(Seq))
-       EBFDR=rep(0,length(Seq))
-       DETPNum=rep(0,length(Seq))
-    EBTPNum=rep(0,length(Seq))
-    DEFDNum=rep(0,length(Seq))
-    EBFDNum=rep(0,length(Seq))
-       for (i in 1:length(Seq)){
-               DESeqOnes=names(DESeqP)[DESeqP<=Seq[i]]
-               if (length(FDR)==0) EBOnes=names(EBZ)[EBZ>=crit.fun(1-EBZ, Seq[i])]
-               else if (FDR=="H") EBOnes=names(EBZ)[EBZ>=(1-Seq[i])]
-                       else EBOnes=names(EBZ)[EBZ>=FDR[i]]
-
-               DETPNum[i]=sum(DESeqOnes%in%TrueDE)
-               EBTPNum[i]=sum(EBOnes%in%TrueDE)
-               DEFDNum[i]=sum(!DESeqOnes%in%TrueDE)
-               EBFDNum[i]=sum(!EBOnes%in%TrueDE)
-               
-               DETPR[i]=DETPNum[i]/length(TrueDE)
-               EBTPR[i]=EBTPNum[i]/length(TrueDE)
-               DEFDR[i]=DEFDNum[i]/length(TrueDE)
-               EBFDR[i]=EBFDNum[i]/length(TrueDE)
-       }
-       plot(Seq,DETPR,ylim=c(0,1),xlim=c(0,.5),type="l",col="red", main=paste(main, "TPR"),xlab="controled FDR level", ylab="TPR",lwd=2)
-       lines(Seq,EBTPR,col="blue",lwd=2)
-       legend("bottomright",lwd=2, col=c("red","blue"), c("DESeq","EBSeq"))
-
-       plot(Seq,DEFDR,ylim=c(0,1),xlim=c(0,.5),type="l",col="red", main=paste(main, "FDR"),xlab="controled FDR level", ylab="TPR",lwd=2)
-       lines(Seq,EBFDR,col="blue",lwd=2)
-       legend("topleft", lwd=2, col=c("red","blue"), c("DESeq","EBSeq"))
-
-
-       output=cbind( DETPR,EBTPR, DEFDR,EBFDR,DETPNum,EBTPNum,DEFDNum,EBFDNum)
-}
-