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

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

diff --git a/EBSeq/R/LogN.R b/EBSeq/R/LogN.R
deleted file mode 100644 (file)
index 7767b93..0000000
--- a/EBSeq/R/LogN.R
+++ /dev/null
@@ -1,45 +0,0 @@
-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
-    }
-