numbat (version 1.3.2-1)

run_joint_hmm: Run joint HMM on a pseudobulk profile

Description

Run joint HMM on a pseudobulk profile

Usage

run_joint_hmm(
  pAD,
  DP,
  p_s,
  Y_obs = 0,
  lambda_ref = 0,
  d_total = 0,
  theta_min = 0.08,
  theta_neu = 0,
  bal_cnv = TRUE,
  phi_del = 2^(-0.25),
  phi_amp = 2^(0.25),
  phi_bamp = phi_amp,
  phi_bdel = phi_del,
  alpha = 1,
  beta = 1,
  mu = 0,
  sig = 1,
  t = 1e-05,
  gamma = 18,
  prior = NULL,
  exp_only = FALSE,
  allele_only = FALSE,
  classify_allele = FALSE,
  phasing = TRUE,
  debug = FALSE
)

Arguments

pAD

integer vector Paternal allele counts

DP

integer vector Total alelle counts

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

phi_bamp

numeric Expected fold change for balanced amplification

phi_bdel

numeric Expected fold change for balanced deletion

mu

numeric Global expression bias

sig

numeric Global expression variance

t

numeric Transition probability between copy number states

gamma

numeric Overdispersion in the allele-specific expression

exp_only

logical Whether to only use expression data

allele_only

logical Whether to only use allele data