getAmpDel: Fraction of amplification or deletion in the genome
In CHAT: Clonal Heterogeneity Analysis Tool

Description Usage Arguments Value Author(s) Examples

This function returns the fraction of amplified or deleted regions in the genome.

1	getAmpDel(oo, sam.dat)

`oo`	Origin Cluster, as returned from `getOrigin()`
`sam.dat`	numeric matrix, as returned from `getSeg()` or `getSegChr()`

a vector containing two numeric numbers: fraction of amplification and deletion.

Bo Li

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)
getAmpDel(oo,dd.dat)