Description Usage Arguments Value Author(s) Examples
This function returns the fraction of loss-of-heterozygosity regions in the genome
1 | getLOH(cali, sam.dat, para)
|
cali |
list, returned by |
sam.dat |
numeric matrix, as returned from |
para |
list, parameters returned from |
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 |
Bo Li
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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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