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

[rsem.git] / EBSeq / R / f0.R

diff --git a/EBSeq/R/f0.R b/EBSeq/R/f0.R
deleted file mode 100644 (file)
index a3ec550..0000000
--- a/EBSeq/R/f0.R
+++ /dev/null
@@ -1,22 +0,0 @@
-f0 <-
-function(Input, AlphaIn, BetaIn, EmpiricalR, NumOfGroups, log)
-{      
-                
-               BetaVect=do.call(c,sapply(1:length(BetaIn),function(i)rep(BetaIn[i],NumOfGroups[i]),simplify=F))
-               SampleNum=dim(Input)[2]
-               #Product part
-               ChooseParam1=round(Input+EmpiricalR-1)
-               roundInput=round(Input)
-               EachChoose=sapply(1:SampleNum, function(i)lchoose(ChooseParam1[,i], roundInput[,i]))
-               
-               SumEachIso=rowSums(Input)
-               param1=AlphaIn + rowSums(EmpiricalR)
-               param2=BetaVect + SumEachIso
-               LogConst=rowSums(EachChoose)+lbeta(param1, param2)-lbeta(AlphaIn, BetaVect)
-
-
-               if (log==F) FinalResult=exp(LogConst)
-               if (log==T) FinalResult=LogConst
-    FinalResult
-}
-