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

In veltenlab/mitoClone: Clonal tracking in single-cell RNA-seq data using mitochondrial and somatic mutations

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 blacklist of variants that were observed in several individuals and that therefore are unlikely to represent true somatic variants (e.g. RNA editing events). These blacklists are created using mutationCallsFromCohort

Usage

mutationCallsFromBlacklist(
  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),
  blacklists.use = blacklists,
  max.var.na = 0.5,
  max.cell.na = 0.95,
  ...
)

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.
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
...	Parameters passed to mutationCallsFromMatrix
blacklists	Blacklists to use **explanations ben**

Value

An object of class mutationCalls

veltenlab/mitoClone documentation built on April 18, 2021, 5:19 a.m.