Included EBSeq for downstream differential expression analysis

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

diff --git a/EBSeq/R/f0.R b/EBSeq/R/f0.R
new file mode 100644 (file)
index 0000000..a3ec550
--- /dev/null
+++ b/EBSeq/R/f0.R
@@ -0,0 +1,22 @@
+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
+}
+