calc_allele_lik_s2: Calculate allele likelihoods for 2-state allele HMM

In hahmmr: Haplotype-Aware Hidden Markov Model for RNA

Calculate allele likelihoods for 2-state allele HMM

Description

Calculate allele likelihoods for 2-state allele HMM

Usage

calc_allele_lik_s2(pAD, DP, R, p_s, theta, gamma = 20, r = 0.015)

Arguments

pAD	integer vector Paternal allele counts
DP	integer vector Total alelle counts
R	numeric vector Variant mapping bias direction
p_s	numeric vector Phase switch probabilities
theta	numeric Haplotype imbalance
gamma	numeric Overdispersion in the allele-specific expression

Value

numeric vector Allele likelihoods

hahmmr documentation built on Oct. 26, 2023, 1:08 a.m.