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

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

Create a mutationCalls objects from nucleotide base calls and defines a exclusionlist (cohort)

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 exclusionlist derived from the original Velten et al. 2021 dataset is available internal and can be used on single individuals using mutationCallsFromExclusionlist

Usage

mutationCallsFromCohort(
  BaseCounts,
  sites,
  patient,
  MINREADS = 5,
  MINCELL = 20,
  MINFRAC = 0.1,
  MINCELLS.PATIENT = 10,
  MINFRAC.PATIENT = 0.01,
  MINFRAC.OTHER = 0.1,
  USE.REFERENCE = TRUE,
  genome = "hg38"
)

Arguments

BaseCounts	A list of base call matrices (one matrix per cell) as produced by baseCountsFromBamList or bam2R_10x.
sites	Vector specifying genomic regions, defaults to the entire mitochondrial genome. Excepts a string but may be included as a GRanges object.
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
MINFRAC.PATIENT	Minimum fraction of mutant cells per patient to classify the mutation as relevant in that patient
MINFRAC.OTHER	Minimum fraction of mutant cells identified in a second patient for the mutation to be excluded. Fraction relative to the fraction of of cells from the patient where a variant is enriched.
USE.REFERENCE	Boolean. The variant calls will be of the format REF>ALT where REF is decided based on the selected genome annotation. If set to FALSE, the reference allele will be the most abundant.
genome	The mitochondrial genome of the sample being investigated. Please note that this is the UCSC standard chromosome sequence. Default: hg38.

Value

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

Examples

sites.gr <- GenomicRanges::GRanges("chrM:1-15000")
BaseCounts <- bam2R_10x(file = system.file("extdata",
"mm10_10x.bam", package="mitoClone2"), sites=sites.gr)
mutCalls <- mutationCallsFromCohort(BaseCounts,
patient=c('sample2','sample1','sample2','sample2','sample1','sample2'),
MINCELL=1, MINFRAC=0, MINCELLS.PATIENT=1, genome='mm10',
sites=sites.gr)

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