CHAT (version 1.1)

getLOH: Fraction of loss-of-heterozygosity

Description

This function returns the fraction of loss-of-heterozygosity regions in the genome

Usage

getLOH(cali, sam.dat, para)

Arguments

cali

list, returned by getSumDist()

sam.dat

numeric matrix, as returned from getSeg() or getSegChr()

para

list, parameters returned from getPara()

Value

list, inherited from getSumDist() with additional elements:

del.loh

fraction of LOH with deletions

cn.loh

fraction of copy neutral LOH

amp.3

fraction of hemizygous amplification

Examples

data(A0SD.BAF)
data(A0SD.LRR)
seg.dat=c()
for(CHR in c(8,9,10)){
	baf=A0SD.BAF[A0SD.BAF[,2]==CHR,]
	lrr=A0SD.LRR[A0SD.LRR[,2]==CHR,]
	x=getSegChr(baf,lrr)
	seg.dat=rbind(seg.dat,x)
}
dd.dat=seg.dat[,2:8]
rownames(dd.dat)=seg.dat[,1]
mode(dd.dat)='numeric'
para=getPara()
oo=getOrigin(dd.dat,para=para)
cali=getSampleAGP(dd.dat,oo,para=para)
getLOH(cali,dd.dat,para=para)