run_allele_hmm_s3: Run a 3-state allele HMM

In hahmmr: Haplotype-Aware Hidden Markov Model for RNA

Run a 3-state allele HMM

Description

Run a 3-state allele HMM

Usage

run_allele_hmm_s3(
  pAD,
  DP,
  R,
  p_s,
  t = 1e-05,
  theta_min = 0.08,
  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
t	numeric Transition probability between copy number states
theta_min	numeric Minimum haplotype frequency deviation threshold
gamma	numeric Overdispersion in the allele-specific expression

Value

character vector Decoded states

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