R/applyCNPmask.R

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

applyCNPmask<-function(segtable,chrom,startPos,endPos,startProbe,endProbe,
	eventIndex,masktable,maskchrom,maskstart,maskend,maskindex,mincover=1,
	indexvals=c(-1,1)){
	breakCNPs<-by(segtable,INDICES=as.factor(segtable[,chrom]),
		FUN=breakIntoCNPs.chrom,chrom=chrom,startPos=startPos,endPos=endPos,
		startProbe=startProbe,endProbe=endProbe,eventIndex=eventIndex,
		cnptable=masktable,cnpchrom=maskchrom,cnpstart=maskstart,
		cnpend=maskend,cnpindex=maskindex,mincover=mincover,indexvals=indexvals,
		simplify=T)
	myCNPs<-matrix(ncol=3,byrow=T,data=unlist(lapply(breakCNPs,t)))	
	dimnames(myCNPs)[[2]]<-c("StartProbe","EndProbe","toremove")
	return(as.matrix(myCNPs))
}