Fraction of loss-of-heterozygosity

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Description

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

Usage

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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

Author(s)

Bo Li

Examples

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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)

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