baseCountsFromBamList: Create a list object from a list of single-cell BAM files...

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

Create a list object from a list of single-cell BAM files where each contains a matrix of the of AGCT nt counts at chosen sites

Description

Uses the deepSNV package to count nucleotide frequencies at every position in the mitochondrial genome for every cell.

Usage

baseCountsFromBamList(
  bamfiles,
  sites = "chrM:1-16569",
  ncores = 1,
  ignore_nonstandard = FALSE
)

Arguments

bamfiles	A character vector specifying the bam file paths
sites	String specifying genomic regions, defaults to the entire mitochondrial genome
ncores	Number of threads to use for the computation. Default 1
ignore_nonstandard	Ignore basecalls that are not AGCTN

Value

A list of base count matrices which can serve as an input to mutationCallsFromExclusionlist or mutationCallsFromCohort

Examples

bamCounts <- baseCountsFromBamList(bamfiles =
list(system.file("extdata", "mm10_10x.bam",
package="mitoClone2")),sites="chrM:1-15000", ncores=1)

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