vafEst: Return the allele frequencies of SSNVs for each allele state

In SunPathLab/Butte: BoUnds of Time Till Expansion, inferring the SCNA arrival time in the somatic evolution toward the most recent common ancestor of tumor sample(s).

Return the allele frequencies of SSNVs for each allele state

Description

Given a SCNA configuration Nt (total copy) and Nb (minor copy), as well as the tumor purity and prevalence of the SCNA, this function returns the expected allele frequencies for possible allele states.

Usage

vafEst(ncmut = "all", nt, nb, pu, pa = 1)

Arguments

ncmut	the number of copies for the mutation, default print for "all"
nt	total copy number
nb	copy number of minor allele
pu	tumor purity
pa	prevalence of the SCNA WITHIN the tumor content, default 1 (clonal)

Value

a named vector of expected allele frequency at each allele state

SunPathLab/Butte documentation built on Sept. 19, 2023, 9:42 a.m.