run_group_hmms: Run multiple HMMs

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

Run multiple HMMs

Description

Run multiple HMMs

Usage

run_group_hmms(
  bulks,
  t = 1e-04,
  gamma = 20,
  alpha = 1e-04,
  min_genes = 10,
  common_diploid = TRUE,
  diploid_chroms = NULL,
  allele_only = FALSE,
  retest = TRUE,
  run_hmm = TRUE,
  segs_loh = NULL,
  exclude_neu = TRUE,
  ncores = 1,
  verbose = FALSE,
  debug = FALSE
)

Arguments

bulks	dataframe Pseudobulk profiles
t	numeric Transition probability
gamma	numeric Dispersion parameter for the Beta-Binomial allele model
alpha	numeric P value cut-off to determine segment clusters in find_diploid
common_diploid	logical Whether to find common diploid regions between pseudobulks
diploid_chroms	character vector Known diploid chromosomes to use as baseline
allele_only	logical Whether only use allele data to run HMM
retest	logcial Whether to retest CNVs
run_hmm	logical Whether to run HMM segments or just retest
ncores	integer Number of cores

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