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

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

diff --git a/EBSeq/R/DenNHistTable.R b/EBSeq/R/DenNHistTable.R
deleted file mode 100644 (file)
index e3a6855..0000000
--- a/EBSeq/R/DenNHistTable.R
+++ /dev/null
@@ -1,38 +0,0 @@
-DenNHistTable <-
-function(QList,Alpha,Beta,AList="F")
-{      
-       par(mfrow=c(3,4))
-       plot(1, type="n", axes=F, xlab="", ylab="", main="No 3' end  No 5' end",cex.main=1)
-       plot(1, type="n", axes=F, xlab="", ylab="",main="With 3' end No 5' end",cex.main=1)
-       plot(1, type="n", axes=F, xlab="", ylab="",main="With 5' end No 3' end",cex.main=1)
-       for (i in c(1,2,4,6,8)){
-                alpha.use=Alpha
-       hist(QList[[i]][QList[[i]]<.98&QList[[i]]>0],prob=T,col="blue",breaks=100,main=ifelse(i==1,"With 5' end With 3' end",""),cex.main=1, xlim=c(0,1),xlab=paste("Q alpha=",round(alpha.use,2)," beta=",round(Beta[i],2),sep=""))
-       if(i==1)mtext("Ng=1",side=4, cex=1)
-       if(i==8)mtext("Ng=2", side=4,cex=1)
-       tmpSize=length(QList[[i]][QList[[i]]<.98])
-
-        tmpseq=seq(0.001,1,length=1000)
-       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,cex=.5)
-}
-       
-       for (i in c(3,5,7,9)){
-                alpha.use=Alpha
-       hist(QList[[i]][QList[[i]]<.98&QList[[i]]>0],prob=T,col="blue",breaks=100,main=ifelse(i==1,"With 5' end With 3' end exons",""),xlim=c(0,1),xlab=paste("Q alpha=",round(alpha.use,2)," beta=",round(Beta[i],2),sep=""))
-       if(i==9)mtext("Ng=3", side=4,cex=1)
-
-       tmpSize=length(QList[[i]][QList[[i]]<.98])
-
-        tmpseq=seq(0.001,1,length=1000)
-       ll=tmpseq
-                lines(ll,dbeta(ll,alpha.use,Beta[i]),col="green",lwd=2)
-       legend("topright",c("Data","Fitted density"),col=c("blue","green"),cex=.5, lwd=2)
-}
-
-
-
-
-       }
-