hahmmr (version 1.0.0)

run_allele_hmm_s3: 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
)

Value

character vector Decoded states

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