findClones: Find Clones

In jlaffy/infercna: Infer Copy Number Alterations And Clonality In (Single-Cell) RNA-seq Data

Find Clones

Description

Assign cells to genetic subclones from their inferred CNA profiles. You can compute their CNA profiles using infercna::infercna().

Usage

findClones(
  m,
  prob = 0.95,
  coverage = 0.8,
  mode.size = 10,
  clone.size = 3,
  by = "chr",
  bySampling = FALSE,
  nsamp = 2000,
  force.tries = FALSE,
  verbose = FALSE,
  ...
)

Arguments

m	a matrix of genes X cells (variables X observations) containing CNA values.
prob	a numeric value >= 0 and <= 1; the minimum posterior probability required for an observation to be assigned to a mode. Default: 0.95
coverage	the fraction of observations that must have a posterior probability higher than <prob> to one of two modes in order for the distribution to qualify as bimodal. Default: 0.8
mode.size	the minimum number of observations required to define a mode. Default: 10
clone.size	the minimum number of cells required to define a clone. Default: 3
by	PARAM_DESCRIPTION, Default: 'chr'

Value

OUTPUT

jlaffy/infercna documentation built on Jan. 26, 2024, 11:24 p.m.