Fraction of amplification or deletion in the genome

Share:

Description

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

Usage

1
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.

Author(s)

Bo Li

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
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)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.