calculateRelatednessMutations: Calculate relatedness scores for paired tumours

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

Calculate relatedness scores for paired tumours

Description

Calculates the relatedness scores and (optionally) p-values for paired tumours from mutation data

Usage

calculateRelatednessMutations(
  mutationTable,
  pairs,
  additionalMutations = NULL,
  nAdditionalSamples = 0,
  reference = NULL,
  excludeChromosomes = "chrY",
  scaleAFs = FALSE
)

Arguments

mutationTable	A table of mutations in each sample and their allele frequencies.
pairs	A table of paired samples from the dataset, to test for relatedness.
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.
reference	A numeric vector of pair scores comprising the reference distribution, generated from the makeReferenceMutations function. If omitted, p-value calculation will be skipped.
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 data frame listing the tumour pairs contained in pairs, their relatedness scores and p-values for relatedness.

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