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

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

diff --git a/EBSeq/R/TopCts.R b/EBSeq/R/TopCts.R
deleted file mode 100644 (file)
index 137977c..0000000
--- a/EBSeq/R/TopCts.R
+++ /dev/null
@@ -1,23 +0,0 @@
-TopCts <-
-function(pvalue, PP=NULL, TrueNames, TopNum){
-       NumOfMethods=ncol(pvalue)
-       puse=pvalue
-       if(1%in%PP)puse[,PP==1]=1-pvalue[,PP==1]
-       #puse.list=data.frame(puse)
-       FD=matrix(rep(0,NumOfMethods*TopNum),ncol=NumOfMethods)
-#      Rank=apply(puse,2,rank)
-#      for(i in 1:TopNum)
-#              FD[i,]=sapply(1:NumOfMethods, function(j)sum(!rownames(Rank)[Rank[,j]<=i]%in%TrueNames))        
-#      FD=sapply(1:TopNum, function(i)sapply(1:NumOfMethods, function(j)sum(!rownames(Rank)[Rank[,j]<=i]%in%TrueNames)))
-       for (s in 1:NumOfMethods){
-               tmp=puse[,s]
-               names(tmp)=rownames(puse)
-               sorttmp=sort(tmp)
-               for( c in 2:TopNum)
-                       FD[c, s]=FD[(c-1),s]+as.numeric(!names(sorttmp)[c]%in%TrueNames)
-       }
-       FD
-       #matplot(TopNum,FD,type="l",ylim=c(0,1),xlab="Top DE selected", ylab="FDR")
-       #legend("rightbottom",col=1:TopNum, lty=1:TopNum, names)
-       }
-