Included EBSeq for downstream differential expression analysis

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

diff --git a/EBSeq/R/LogN.R b/EBSeq/R/LogN.R
new file mode 100644 (file)
index 0000000..7767b93
--- /dev/null
+++ b/EBSeq/R/LogN.R
@@ -0,0 +1,45 @@
+LogN <-
+function(Input, InputSP, EmpiricalR, EmpiricalRSP, NumOfEachGroup, AlphaIn, BetaIn,  PIn, NoneZeroLength)
+{
+    #2 condition case (skip the loop then maybe run faster? Code multi condition cases later)
+
+        #For each gene (m rows of Input---m genes)
+        #Save each gene's F0, F1 for further likelihood calculation. 
+  
+        #Get F0 for EE
+        F0=f0(Input,  AlphaIn, BetaIn, EmpiricalR, NumOfEachGroup, log=F)
+        #Get F1 for DE
+        F1=f1(InputSP[[1]], InputSP[[2]], AlphaIn, BetaIn, EmpiricalRSP[[1]],EmpiricalRSP[[2]], NumOfEachGroup, log=F)
+
+        #Get z
+               #Use data.list in logfunction
+        
+               z.list=PIn*F1/(PIn*F1+(1-PIn)*F0)
+               zNaNName=names(z.list)[is.na(z.list)]
+               zGood=which(!is.na(z.list))
+               ###Update P
+        #PFromZ=sapply(1:NoneZeroLength,function(i) sum(z.list[[i]])/length(z.list[[i]]))
+        PFromZ=sum(z.list[zGood])/length(z.list[zGood])
+        F0Good=F0[zGood]
+               F1Good=F1[zGood]
+               ### MLE Part ####
+        # Since we dont wanna update p and Z in this step
+        # Each Ng for one row
+               
+               NumGroupVector=rep(c(1:NoneZeroLength),NumOfEachGroup)
+               
+               NumGroupVector.zGood=NumGroupVector[zGood]
+               NumOfEachGroup.zGood=tapply(NumGroupVector.zGood,NumGroupVector.zGood,length)
+
+        StartValue=c(AlphaIn, BetaIn,PIn)
+                    
+               Result<-optim(StartValue,Likefun,InputPool=list(InputSP[[1]][zGood,],InputSP[[2]][zGood,],Input[zGood,],z.list[zGood], NoneZeroLength,EmpiricalR[zGood, ],EmpiricalRSP[[1]][zGood,], EmpiricalRSP[[2]][zGood,], NumOfEachGroup.zGood))
+        #LikeOutput=Likelihood( StartValue, Input , InputSP , PNEW.list, z.list)
+               AlphaNew= Result$par[1]
+               BetaNew=Result$par[2:(1+NoneZeroLength)]
+        PNew=Result$par[2+NoneZeroLength]
+               ##
+        Output=list(AlphaNew=AlphaNew,BetaNew=BetaNew,PNew=PNew,ZNew.list=z.list,PFromZ=PFromZ, zGood=zGood, zNaNName=zNaNName,F0Out=F0Good, F1Out=F1Good)
+        Output
+    }
+