CHAT (version 1.1)

getAmpDel: Fraction of amplification or deletion in the genome

Description

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

Usage

getAmpDel(oo, sam.dat)

Arguments

oo

Origin Cluster, as returned from getOrigin()

sam.dat

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

Value

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

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)
getAmpDel(oo,dd.dat)