getLOH: Fraction of loss-of-heterozygosity

In CHAT: Clonal Heterogeneity Analysis Tool

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

Author(s)

Bo Li

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)

CHAT documentation built on May 29, 2017, 10:32 p.m.