# Calculate emprical raw regions from \code{myDiff} object.
getPeaks=function(allMyDiff, pcutoff=0.1, dist=100){
print("raw myDiff:")
print(dim(allMyDiff))
myDiff=allMyDiff[allMyDiff$ppvalue<=pcutoff,]
probes.dist=diff(myDiff$pend)
print(paste("max cpgs dist for region definition:", dist))
bpoints=which(probes.dist>=dist | probes.dist<0)
first.peak=c(as.character(myDiff[1,1]), myDiff[1,2],end=myDiff[bpoints[1],3])
mid.peaks=cbind(myDiff[(bpoints[-length(bpoints)]+1),1:2],end=myDiff[bpoints[-1],3])
last.idx=bpoints[length(bpoints)]+1
last.peak=c(as.character(myDiff[last.idx,1]), myDiff[last.idx,2], end=myDiff[nrow(myDiff),3])
peaks=as.data.frame(rbind(first.peak, mid.peaks, last.peak))
colnames(peaks)=c("rchr","rstart","rend")
peaks
}
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