Included EBSeq for downstream differential expression analysis

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

diff --git a/EBSeq/R/Likefun.R b/EBSeq/R/Likefun.R
new file mode 100644 (file)
index 0000000..ebe05ab
--- /dev/null
+++ b/EBSeq/R/Likefun.R
@@ -0,0 +1,26 @@
+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))
+}
+