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

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

diff --git a/EBSeq/R/DenNHist.R b/EBSeq/R/DenNHist.R
deleted file mode 100644 (file)
index 76e5d60..0000000
--- a/EBSeq/R/DenNHist.R
+++ /dev/null
@@ -1,20 +0,0 @@
-DenNHist <-
-function(QList,Alpha,Beta,name,AList="F",GroupName)
-{
-    if(!is.list(QList)) QList=list(QList)      
-       for (i in 1:length(QList)){
-               if (AList=="F") alpha.use=Alpha
-                       if(AList=="T")  alpha.use=Alpha[i]
-       hist(QList[[i]][QList[[i]]<.98&QList[[i]]>0],prob=T,col="blue",breaks=100,main=paste(GroupName[i],name,sep=" "),xlim=c(0,1),xlab=paste("Q alpha=",round(alpha.use,2)," beta=",round(Beta[i],2),sep=""))
-       tmpSize=length(QList[[i]][QList[[i]]<.98])
-        tmpseq=seq(0.001,1,length=1000)
-        #tmpdensity=dbeta(tmpseq,AlphaResult,BetaResult[i])
-        #points(tmpseq,tmpdensity, type="l",col="green")
-       #ll=dbeta(tmpseq,Alpha,Beta[i])
-       ll=tmpseq
-                lines(ll,dbeta(ll,alpha.use,Beta[i]),col="green",lwd=2)
-       legend("topright",c("Data","Fitted density"),col=c("blue","green"),lwd=2)
-}
-       
-       }
-