retest_bulks: retest consensus segments on pseudobulks
In numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

retest_bulks

R Documentation

retest consensus segments on pseudobulks

Description

retest consensus segments on pseudobulks

Usage

retest_bulks(
  bulks,
  segs_consensus = NULL,
  t = 1e-05,
  min_genes = 10,
  gamma = 20,
  nu = 1,
  use_loh = FALSE,
  diploid_chroms = NULL,
  ncores = 1,
  exclude_neu = TRUE,
  min_LLR = 5
)

Arguments

`bulks`	dataframe Pseudobulk profiles
`segs_consensus`	dataframe Consensus segments
`use_loh`	logical Whether to use loh in the baseline
`diploid_chroms`	vector User-provided diploid chromosomes