find_common_diploid: Find the common diploid region in a group of pseudobulks

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

Find the common diploid region in a group of pseudobulks

Description

Find the common diploid region in a group of pseudobulks

Usage

find_common_diploid(
  bulks,
  grouping = "clique",
  gamma = 20,
  theta_min = 0.08,
  t = 1e-05,
  fc_min = 2^0.25,
  alpha = 1e-04,
  min_genes = 10,
  ncores = 1,
  debug = FALSE,
  verbose = TRUE
)

Arguments

bulks	dataframe Pseudobulk profiles (differentiated by "sample" column)
grouping	logical Whether to use cliques or components in the graph to find dipoid cluster
gamma	numeric Dispersion parameter for the Beta-Binomial allele model
theta_min	numeric Minimum imbalance threshold
t	numeric Transition probability
fc_min	numeric Minimum fold change to call quadruploid cluster
alpha	numeric FDR cut-off for q values to determine edges
ncores	integer Number of cores to use

Value

list Ploidy information

numbat documentation built on May 29, 2024, 1:29 a.m.