R/breakIntoCNPs.chrom.R

In CNprep: Pre-Process DNA Copy Number (CN) Data for Detection of CN Events

breakIntoCNPs.chrom<-function(segtable,chrom,startPos,endPos,startProbe,
	endProbe,eventIndex,cnptable,cnpchrom,cnpstart,cnpend,cnpindex,mincover,
	indexvals){
	toremove<-rep(0,nrow(segtable))
	segtable<-cbind(segtable,toremove)
	chr<-segtable[1,chrom]
	if(sum(segtable[,eventIndex]!=0)==0|sum(cnptable[,cnpchrom]==chr)==0)
		return(as.matrix(segtable[,c(startProbe,endProbe,"toremove")]))
	cnpsinchr<-cnptable[cnptable[,cnpchrom]==chr,,drop=F]
	for(i in indexvals)
		if(sum(segtable[,eventIndex]==i)>0&sum(cnpsinchr[,cnpindex]==i)>0){
		acnpinchr<-cnpsinchr[cnpsinchr[,cnpindex]==i,,drop=F]
		amps<-which(segtable[,eventIndex]==i)
		segstartmat<-matrix(ncol=nrow(acnpinchr),
			data=rep(segtable[amps,startPos],nrow(acnpinchr)))
		segendmat<-matrix(ncol=nrow(acnpinchr),
			data=rep(segtable[amps,endPos],nrow(acnpinchr)))
		cnpstartmat<-t(matrix(ncol=length(amps),
			data=rep(acnpinchr[,cnpstart],length(amps))))
		cnpendmat<-t(matrix(ncol=length(amps),
			data=rep(acnpinchr[,cnpend],length(amps))))
		cnpcover<-rowSums(pmax(matrix(nrow=nrow(cnpendmat),
			ncol=ncol(cnpendmat),data=0),(pmin(segendmat,cnpendmat)-
			pmax(segstartmat,cnpstartmat)+1)))/
			(segtable[amps,endPos]-segtable[amps,startPos]+1)
		toremove[amps[cnpcover>mincover]]<-1
	}
	segtable[,"toremove"]<-toremove
	if(sum(toremove)>0)segtable[,c(startProbe,endProbe)]<-
		breakIntoGaps(segtable,"toremove",startProbe,endProbe)
	return(as.matrix(segtable[,c(startProbe,endProbe,"toremove")]))
}