getHets: Obtain germline heterozygous markers

In Shicheng-Guo/CHAT: Clonal Heterogeneity Analysis Tool

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.

Details

When paired.baf is given, any marker has germline BAF>=1-thr or BAF<=thr are considered as homozygous. If paired.baf is missing, then in non-LOH regions, the method uses the same criteria to select heterozygous markers; in LOH regions, 1/3 of the markers are randomly selected as germline heterozygous.

Value

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

Author(s)

Bo Li

Examples

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

Shicheng-Guo/CHAT documentation built on Oct. 30, 2019, 11:55 p.m.