R/f0.R

In EBSeq: An R package for gene and isoform differential expression analysis of RNA-seq data

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)
		EachChoose0=matrix(sapply(1:SampleNum, function(i)lchoose(ChooseParam1[,i], roundInput[,i])),ncol=SampleNum)
		# numerical approximation to rescue -Inf ones
		NoNegInfMin=min(EachChoose0[which(EachChoose0!=-Inf)])
		NoPosInfMax=max(EachChoose0[which(EachChoose0!=Inf)])
		EachChoose=EachChoose0
		EachChoose[which(EachChoose0==-Inf, arr.ind=T)]=NoNegInfMin
		EachChoose[which(EachChoose0==Inf, arr.ind=T)]=NoPosInfMax
	
		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
}