mutationCallsFromCohort: Create a mutationCalls objects from nucleotide base calls and...

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 measured in single cells from several individuals. Applies two sets of filters: In the first step, filters on coverage to include potentially noisy variants; in the second step, compares allele frequencies between patients to remove variants that were observed in several individuals and that therefore are unlikely to represent true somatic variants (e.g. RNA editing events). The blacklist derived from the MutaSeq dataaset is available in blacklist and can be used on single individuals using mutationCallsFromBlacklist

Usage

mutationCallsFromCohort(
  BaseCounts,
  patient,
  MINREADS = 5,
  MINCELL = 20,
  MINFRAC = 0.1,
  MINCELLS.PATIENT = 10,
  MINRELATIVE.PATIENT = 0.01,
  MINRELATIVE.OTHER = 0.1
)

Arguments

BaseCounts	A list of base call matrices (one matrix per cell) as produced by baseCountsFromSingleBam or baseCountsFromBamList
patient	A character vector associating each cell / entry in the BaseCount list with a patient
MINREADS	Minimum number of reads on a site in a single cell to qualify the site as covered
MINCELL	Minimum number of cells across the whole data set to cover a site
MINFRAC	Fraction of reads on the mutant allele to provisionally classify a cell as mutant
MINCELLS.PATIENT	Minimum number of mutant cells per patient to classify the mutation as relevant in that patient, AND
MINRELATIVE.PATIENT	Minimum fraction of mutant cells per patient to classify the mutation as relevant in that patient
MINRELATIVE.OTHER	Minimum fraction of mutant cells identified in a second patient for the mutation to be excluded

Value

A list of mutationCalls objects (one for each patient) and an entry blacklist containing a blacklist of sites with variants in several individuals

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