Description Usage Arguments Details Value Author(s) Examples
Remove uninformative germline homozygous markers for a DNA segment.
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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. |
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.
a vector of indices indicating the positions of heterozygous markers in input baf.
Bo Li
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