Nothing
PCOREiteration <-
function(z,maxmark,minscore=0,nprof=1){
chu<-unique(z[,"chrom"])
chc<-rep(0,length(chu))
for(i in 1:length(chu))chc[i]<-sum(z[,"chrom"]==chu[i])
for(ich in 1:length(chu)){
za<-z[z[,"chrom"]==chu[rev(order(chc))][ich],c("start","end","weight"),drop=F]
za<-za[order(za[,"start"]),,drop=F]
winloci<-matrix(ncol=4,nrow=maxmark,
dimnames=list(NULL,c("chrom","start","end","score")))
winloci[,"chrom"]<-chu[rev(order(chc))][ich]
for(i in 1:maxmark){
if(nrow(za)==0)break
y<-cbind(c(za[,"end"]+1,za[,"start"]),c(-za[,"weight"],za[,"weight"]))
y<-y[order(y[,1]),,drop=F]
cy2<-cumsum(y[,2])
score<-max(cy2)
if(score<minscore)break
stabstart<-y[which.max(cy2),1]
stabend<-min(y[y[,1]>stabstart&y[,2]<=0,1])-1
winloci[i,c("start","end","score")]<-c(stabstart,stabend,score)
if(ich>1)if(((sum(accu[,"score"]>winloci[i,"score"])+i)>=maxmark))break
za<-za[!(za[,"start"]<=stabstart&za[,"end"]>=stabstart),,drop=F]
}
winloci<-winloci[!is.na(winloci[,"score"]),,drop=F]
if(ich==1)accu<-winloci
if(ich>1){
accu<-rbind(accu,winloci)
accu<-accu[accu[,"score"]>=minscore,,drop=F]
accu<-accu[order(accu[,"score"],decreasing=T),,
drop=F][1:min(maxmark,nrow(accu)),,drop=F]
}
}
accu[,"score"]<-accu[,"score"]/nprof
return(accu)
}
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