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

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

diff --git a/EBSeq/R/Likefun.R b/EBSeq/R/Likefun.R
deleted file mode 100644 (file)
index ebe05ab..0000000
--- a/EBSeq/R/Likefun.R
+++ /dev/null
@@ -1,26 +0,0 @@
-Likefun <-
-function(ParamPool, InputPool)
-{
-
-NoneZeroLength=InputPool[[5]]
-AlphaIn=ParamPool[1]
-BetaIn=ParamPool[2:(1+NoneZeroLength)]
-PIn=ParamPool[2+NoneZeroLength]
-ZIn=InputPool[[4]]
-Input=InputPool[[3]]
-Input1=matrix(InputPool[[1]],nrow=nrow(Input))
-Input2=matrix(InputPool[[2]],nrow=nrow(Input))
-RIn=InputPool[[6]]
-RInSP1=matrix(InputPool[[7]],nrow=nrow(Input))
-RInSP2=matrix(InputPool[[8]],nrow=nrow(Input))
-NumIn=InputPool[[9]]
-##Function here
-#LikelihoodFunction<- function(NoneZeroLength){
-       F0=f0(Input, AlphaIn, BetaIn, RIn, NumIn, log=T)
-       F1=f1(Input1, Input2, AlphaIn, BetaIn, RInSP1,RInSP2, NumIn, log=T)
-               F0[F0==Inf]=min(!is.na(F0[F0!=Inf]))
-               F1[F1==Inf]=min(!is.na(F1[F1!=Inf]))
-
-       -sum((1-ZIn)*F0+ (1-ZIn)* log(1-PIn) + ZIn*F1 + ZIn*log(PIn))
-}
-