pullcountsVars: Pull variant counts

In benstory/mitoClone2: Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

Pull variant counts

Description

Pull variant counts

Usage

pullcountsVars(BaseCounts, vars, cells = NULL)

Arguments

BaseCounts	A list of base call matrices (one matrix per cell) as produced by baseCountsFromBamList
vars	Character vector of variants to pull, in format 5643G>T
cells	Character vector for cells to select, or NULL if all cells from the input are to be used

Value

A list with two entries, M (count table on the variant allele) and N (count table on the reference allele)

Examples

load(system.file("extdata/example_counts.Rda",package = "mitoClone2"))
known.variants <- c("9 T>C","12 G>A","13 G>A")
counts.known.vars <- pullcountsVars(example.counts, vars=known.variants)

benstory/mitoClone2 documentation built on Oct. 30, 2024, 3:20 p.m.