calc_allele_LLR: Calculate LLR for an allele HMM

calc_allele_LLRR Documentation

Calculate LLR for an allele HMM

Description

Calculate LLR for an allele HMM

Usage

calc_allele_LLR(pAD, DP, R, p_s, theta_mle, theta_0 = 0, gamma = 20, r = 0.015)

Arguments

pAD

numeric vector Phased allele depth

DP

numeric vector Total allele depth

R

numeric vector Allelic bias direction

p_s

numeric vector Phase switch probabilities

theta_mle

numeric MLE of imbalance level theta (alternative hypothesis)

theta_0

numeric Imbalance level in the null hypothesis

gamma

numeric Dispersion parameter for the Beta-Binomial allele model

Value

numeric Log-likelihood ratio


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