run_joint_hmm: Run joint HMM on a pseudobulk profile
In whtns/numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

run_joint_hmm

R Documentation

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