R/normalComparison.R

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

normalComparison <-
function(normalmedian,normalength,
	tumormedian,tumorlength,normalmad=NULL,normalerror=NULL,tumormad=NULL,
	tumorerror=NULL){
	nisnull<-c(!(is.null(normalmad)|is.null(tumormad)),
		!(is.null(normalerror)|is.null(tumorerror)))
	nsred<-matrix(ncol=2+sum(nisnull),length(normalmedian),
		data=c(normalength,normalmedian,
		if(nisnull[1])normalmad,if(nisnull[2])normalerror),dimnames=list(NULL,
		c("length","mediandev",if(nisnull[1])"segmad",if(nisnull[2])"segerr")))
	nsred<-nsred[order(nsred[,"mediandev"]),,drop=F]
	lnorm<-sum(nsred[,"length"])
	z<-cbind(c(nsred[,"mediandev"],tumormedian),c(nsred[,"length"],
		rep(0,length(tumormedian))),c(rep(0,nrow(nsred)),1:length(tumormedian)))
	z<-z[order(z[,1]),,drop=F]
	z[,2]<-cumsum(z[,2])/lnorm
	z<-z[z[,3]!=0,,drop=F]
	negtail<-z[order(z[,3]),2]
	if(nisnull[1]){
		z<-cbind(c(nsred[,"mediandev"]/nsred[,"segmad"],
  		tumormedian/tumormad),c(nsred[,"length"],
  		rep(0,length(tumormedian))),
			c(rep(0,nrow(nsred)),1:length(tumormedian)))
		z<-z[order(z[,1]),,drop=F]
		z[,2]<-cumsum(z[,2])/lnorm
		z<-z[z[,3]!=0,,drop=F]
		negtailnormad<-z[order(z[,3]),2]
	}
	if(nisnull[2]){
		z<-cbind(c(nsred[,"mediandev"]/nsred[,"segerr"],tumormedian/tumorerror),
			c(nsred[,"length"],rep(0,length(tumormedian))),
			c(rep(0,nrow(nsred)),1:length(tumormedian)))
		z<-z[order(z[,1]),,drop=F]
		z[,2]<-cumsum(z[,2])/lnorm
		z<-z[z[,3]!=0,,drop=F]
		negtailnormerror<-z[order(z[,3]),2]
	}
	return(matrix(ncol=2+sum(nisnull),data=c(lnorm%/%tumorlength,
		negtail,if(nisnull[1])negtailnormad,if(nisnull[2])negtailnormerror),
		dimnames=list(NULL,c("samplesize","negtail",if(nisnull[1])"negtailnormad",
		if(nisnull[2])"negtailnormerror"))))
}