makeReferenceMutations: Generate reference distribution from mutation data

In argymeg/breakclone: Estimating clonal relatedness probability between tumour pairs

Generate reference distribution from mutation data

Description

Generates the reference distribution of concordance scores from unpaired tumours for a given dataset.

Usage

makeReferenceMutations(
  mutationTable,
  pairs,
  patients = NULL,
  delimiter = NULL,
  additionalMutations = NULL,
  nAdditionalSamples = 0,
  excludeChromosomes = "Y",
  scaleAFs = FALSE
)

Arguments

mutationTable	A table of mutations in each sample and their allele frequencies.
pairs	A table of paired samples from the dataset. All tumours present in this table will be paired with all tumours from other patients.
patients	A character vector of patient IDs, parallel to the pairs table, used to prevent tumours originating from the same patient from being used in the reference distribution (optional)
delimiter	A character separating patient IDs from tumour-specific identifiers in the sample IDs. Ignored if patients is provided.
additionalMutations	A table of mutations to be taken into account when calculating population frequencies. At a minimum, a table of the mutations in the population being studied. This is more informative when tumour type-specific mutations are included from external sources (e.g. TCGA).
nAdditionalSamples	The number of samples used to derive the additional mutations table.
excludeChromosomes	The name(s) of any chromosomes to be excluded.
scaleAFs	Scale AFs per-sample by the highest AF within each sample. Only recommended for data with significant normal contamination that you are confident contains at least one clonal mutation per sample.

Value

A numeric vector of pair scores comprising the reference distribution.

argymeg/breakclone documentation built on Nov. 9, 2024, 7:12 p.m.