run_joint_hmm_s7: Run 7-state joint HMM on a pseudobulk profile
In hahmmr: Haplotype-Aware Hidden Markov Model for RNA

run_joint_hmm_s7

R Documentation

Run 7-state joint HMM on a pseudobulk profile

Description

Run 7-state joint HMM on a pseudobulk profile

Usage

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