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

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

diff --git a/EBSeq/R/LikefunMulti.R b/EBSeq/R/LikefunMulti.R
deleted file mode 100644 (file)
index 510cb1e..0000000
--- a/EBSeq/R/LikefunMulti.R
+++ /dev/null
@@ -1,28 +0,0 @@
-LikefunMulti <-
-function(ParamPool, InputPool)
-{
-
-NoneZeroLength=InputPool[[4]]
-AlphaIn=ParamPool[1]
-BetaIn=ParamPool[2:(1+NoneZeroLength)]
-PIn=ParamPool[(2+NoneZeroLength):length(ParamPool)]
-PInAll=c(1-sum(PIn),PIn)
-ZIn=InputPool[[3]]
-Input=InputPool[[2]]
-InputSP=InputPool[[1]]
-RIn=InputPool[[5]]
-RInSP=InputPool[[6]]
-NumIn=InputPool[[7]]
-AllParti=InputPool[[8]]
-PInMat=matrix(rep(1,nrow(Input)),ncol=1)%*%matrix(PInAll,nrow=1)
-##Function here
-FList=sapply(1:nrow(AllParti),function(i)sapply(1:nlevels(as.factor(AllParti[i,])),
-                                               function(j)f0(do.call(cbind,InputSP[AllParti[i,]==j]),AlphaIn, BetaIn, 
-                                       do.call(cbind,RInSP[AllParti[i,]==j]), NumIn, log=T)),
-                                               simplify=F) 
-FPartiLog=sapply(FList,rowSums)
-#FMat=exp(FPartiLog)
-FMat=FPartiLog
--sum(ZIn*(FMat+log(PInMat)))
-}
-