run_allele_hmm_s5 function

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

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

Returns

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)
})