calc_allele_LLR {hahmmr} | R 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
[Package hahmmr version 1.0.0 Index]