Obtain germline heterozygous markers

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Description

Remove uninformative germline homozygous markers for a DNA segment.

Usage

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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

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

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