run_allele_hmm_s5 {hahmmr}

Run a 5-state allele-only HMM - two theta levels

Description

Run a 5-state allele-only HMM - two theta levels

Usage

run_allele_hmm_s5(
  pAD,
  DP,
  p_s,
  t = 1e-05,
  theta_min = 0.08,
  gamma = 20,
  prior = NULL,
  ...
)

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 copy number states

theta_min

numeric Minimum haplotype frequency deviation threshold

gamma

numeric Overdispersion in the allele-specific expression

prior

numeric vector Prior probabilities for each state

...

Additional parameters

Value

character vector Decoded states

Examples

with(bulk_example, {
    run_allele_hmm_s5(pAD = pAD, DP = DP, R = R, p_s = p_s, theta_min = 0.08, gamma = 30)
})