cnaSignal: Calculate the Means of Squared CNA Values

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

Calculate the Means of Squared CNA Values

Description

Calculate the Mean of Squared CNA Values

Usage

cnaSignal(
  cna,
  gene.quantile = NULL,
  cell.quantile.for.genes = NULL,
  refCells = NULL,
  samples = NULL
)

Arguments

cna	a matrix of gene rows by cell columns containing CNA values.
gene.quantile	calculate CNA measures including only top / "hotspot" genes according to their squared CNA values across all cells. Value between 0 and 1 denoting the quantile of genes to include. Default: NULL
refCells	a character vector of cell ids (e.g. normal reference cell ids) to exclude from calculation of cnaHotspotGenes. Only relevant if gene.quantile is not NULL. Default: NULL
samples	if cnaHotspotGenes should be calculated within cell subgroups, provide i) a list of cell id groups, ii) a character vector of sample names to group cells by, iii) TRUE to extract sample names from cell ids and subsequently group. Default: NULL
...	other arguments passed to scalop::unique_sample_names if samples = TRUE.

Value

a numeric vector of CNA signal values or the Mean of Squared CNA values

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