get_allele_hmm_s3: Make a 3-state allele HMM - allow transitions to netural...

In hahmmr: Haplotype-Aware Hidden Markov Model for RNA

Make a 3-state allele HMM - allow transitions to netural state

Description

Make a 3-state allele HMM - allow transitions to netural state

Usage

get_allele_hmm_s3(pAD, DP, R, p_s, t, theta_min, gamma = 20, r = 0.015)

Arguments

pAD	integer vector Paternal allele counts
DP	integer vector Total alelle counts
p_s	numeric vector Phase switch probabilities
t	numeric Transition probability between haplotype states
theta_min	numeric Haplotype imbalance
gamma	numeric Overdispersion in the allele-specific expression
r	numeric Variant mapping bias

Value

HMM object

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