run_joint_hmm_s7 function

Run 7-state joint HMM on a pseudobulk profile

run_joint_hmm_s7(
  pAD,
  DP,
  R,
  p_s,
  Y_obs,
  lambda_ref,
  d_total,
  theta_min = 0.08,
  phi_del = 2^(-0.25),
  phi_amp = 2^(0.25),
  t = 1e-05,
  mu = 0,
  sig = 1,
  gamma = 20,
  r = 0.015,
  debug = FALSE
)

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
• Y_obs: numeric vector Observed gene counts
• lambda_ref: numeric vector Reference expression rates
• d_total: integer Total library size for expression counts
• theta_min: numeric Minimum haplotype imbalance threshold
• phi_del: numeric Expected fold change for deletion
• phi_amp: numeric Expected fold change for amplification
• t: numeric Transition probability between copy number states
• mu: numeric Global expression bias
• sig: numeric Global expression variance
• gamma: numeric Overdispersion in the allele-specific expression
• r: numeric Variant mapping bias
• debug: logical Whether to print debug messages

Returns

character vector Decoded states