run_allele_hmm: allele-only HMM

In whtns/numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

allele-only HMM

Description

allele-only HMM

Usage

run_allele_hmm(
  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

Value

character vector Decoded states

whtns/numbat documentation built on Nov. 8, 2022, 10:48 a.m.