R/breakIntoGaps.R

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

breakIntoGaps<-function(segtable,gapind,StartProbe,EndProbe){
	if(sum(segtable[,gapind])==0)
		return(as.matrix(segtable[,c(StartProbe,EndProbe)]))
	gapstep<-segtable[,gapind]-c(0,segtable[-nrow(segtable),gapind])
	gapstart<-which(gapstep==1)
	gapend<-which(gapstep==-1)-1
	if(length(gapend)<length(gapstart))gapend<-c(gapend,nrow(segtable))
	ranfrac<-runif(n=length(gapend))
	ranfrac[gapstart==1]<-1
	ranfrac[gapend==nrow(segtable)]<-0
	midpoint<-round(ranfrac*segtable[gapstart,StartProbe]+
		(1-ranfrac)*segtable[gapend,EndProbe])
	segtable[(gapend+1)[gapend!=nrow(segtable)],StartProbe]<-
		midpoint[gapend!=nrow(segtable)]
	segtable[(gapstart-1)[gapstart!=1],EndProbe]<-
		ifelse(gapstart[gapstart!=1]!=nrow(segtable),
		midpoint[gapstart!=1]-1,midpoint[gapstart!=1])
	return(as.matrix(segtable[,c(StartProbe,EndProbe)]))
}