calc_allele_LLR: Calculate LLR for an allele HMM

In numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

Calculate LLR for an allele HMM

Description

Calculate LLR for an allele HMM

Usage

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

Arguments

pAD	numeric vector Phased allele depth
DP	numeric vector Total allele depth
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

numbat documentation built on May 29, 2024, 1:29 a.m.