CHAT (version 1.1)

getHets: Obtain germline heterozygous markers

Description

Remove uninformative germline homozygous markers for a DNA segment.

Usage

getHets(baf, paired.baf = NULL, thr = 0.18)

Arguments

baf

numeric vector, original B-allele frequency from a cancer DNA segment

paired.baf

numeric vector, original B-allele frequency from a paired normal DNA segment, with exactly the same length as baf. See details.

thr

numeric, threshold to call germline heterozygous markers.

Value

a vector of indices indicating the positions of heterozygous markers in input baf.

Details

When paired.baf is given, any marker has germline BAF>=1-thr or BAF

Examples

library(CHAT)
data(A0SD.BAF)
baf=A0SD.BAF[1:1000,5]
paired.baf=A0SD.BAF[1:1000,6]
vv=getHets(baf,paired.baf)