numbat (version 1.4.2)

find_common_diploid: 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
)

Value

list Ploidy information

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