Nothing
getHets <- function(baf,paired.baf=NULL,thr=0.18){
#Retrieve heterozygous SNP from BAF file
#if paired.baf is given, the heterozygous markers are estimated using the normal tissue
tag<-c()
window.size<-100 #the size of sliding window
k<-1
while(k+window.size<=length(baf)){
if(!is.null(paired.baf)){ #case with paired samples
tmp<-paired.baf[k:(k+window.size-1)]
hets<-k+which(tmp>=thr&tmp<=(1-thr))-1
tag<-c(tag,sort(hets))
k<-k+window.size
next
}
tmp<-baf[k:(k+window.size-1)]
hets<-k+which(tmp>=thr&tmp<=(1-thr))-1
if(length(hets)<=window.size/10){ #region of LOH
hets<-k+round(runif(round(window.size/3),1,window.size))-1
}
tag<-c(tag,sort(hets))
k<-k+window.size
}
return(tag)
}
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