mutationCallsFromExclusionlist: Create a mutationCalls object from nucleotide base calls...

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

Create a mutationCalls object from nucleotide base calls using a exclusionlist (single individual)

Description

Identifies relevant mitochondrial somatic variants from raw counts of nucleotide frequencies. Applies two sets of filters: In the first step, filters on coverage and minimum allele frequency to exclude potentially noisy variants; in the second step, filters against a exclusionlist of variants that were observed in several individuals and that therefore are unlikely to represent true somatic variants (e.g. RNA editing events). These exclusionlists are created using mutationCallsFromCohort

Usage

mutationCallsFromExclusionlist(
  BaseCounts,
  lim.cov = 20,
  min.af = 0.2,
  min.num.samples = 0.01 * length(BaseCounts),
  min.af.universal = min.af,
  universal.var.cells = 0.95 * length(BaseCounts),
  exclusionlists.use = exclusionlists,
  max.var.na = 0.5,
  max.cell.na = 0.95,
  genome = "hg38",
  ncores = 1,
  ...
)

Arguments

BaseCounts	A list of base call matrices (one matrix per cell) as produced by baseCountsFromBamList
lim.cov	Minimal coverage required per cell for a cell to be classified as covered
min.af	Minimal allele frequency for a cell to be classified as mutant
min.num.samples	Minimal number of cells required to be classified as covered and mutant according to the thresholds set in lim.cov and min.af. Usually specified as a fraction of the total number of cells.
min.af.universal	Minimal allele frequency for a cell to be classified as mutant, in the context of removing universal variants. Defaults to min.af, but can be set to lower values.
universal.var.cells	Maximum number of cells required to be classified as mutant according to the threshold set in min.af.universal. Usually specified as a fraction of the total number of cells; serves to avoid e.g. germline variants.
exclusionlists.use	List of sites to exclude for variants calling. The default exclusionlists object included with this package contains exclude or hardmask in GRanges format. The four exclusionlists included in this case are: "three" (hg38 sites that are part of homopolymer(e.g. AAA) of at least 3 bp in length), "mutaseq" (sites discovered to be overrepresented in AML SmartSeq2 data analysis from Velten et al 2021), "masked" (sites that are softmasked in either the UCSC or Refseq genome annotations), and "rnaEDIT" which are sites that are subjected to RNA-editing according to the REDIportal. These lists can also be input manually by a researcher and provided as either coordinates (as a string) or as a GRanges objects.
max.var.na	Final filtering step: Remove all mutations with no coverage in more than this fraction of cells
max.cell.na	Final filtering step: Remove all cells with no coverage in more than this fraction of mutations
genome	The mitochondrial genome of the sample being investigated. Please note that this is the UCSC standard chromosome sequence. Default: hg38.
ncores	number of cores to use for tabulating potential variants (defaults to 2)
...	Parameters passed to mutationCallsFromMatrix

Value

An object of class mutationCalls

Examples

load(system.file("extdata/example_counts.Rda",package = "mitoClone2"))
Example <- mutationCallsFromExclusionlist(example.counts,
min.af=0.05, min.num.samples=5,
universal.var.cells = 0.5 * length(example.counts),
binarize = 0.1)

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