calculateRelatednessCn: 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 copy number data

Usage

calculateRelatednessCn(
  segmentTable,
  pairs,
  reference = NULL,
  cnType = c("alleleSpecific", "VCF"),
  excludeChromosomes = "Y",
  maxgap = NULL
)

Arguments

segmentTable	A segment table generated by the readAlleleSpecific or readVCFCn functions.
pairs	A table of paired samples from the dataset, to test for relatedness.
reference	A numeric vector of pair scores comprising the reference distribution, generated from the makeReferenceCN function. If omitted, p-value calculation will be skipped.
cnType	The type of copy number data provided. Currently supported options are a custom allele specific data format, and standard copy number VCF files.
excludeChromosomes	The name(s) of any chromosomes to be excluded.
maxgap	The maximum gap between two breakpoints for them to be considered concordant. If unspecified, it is automatically set to 5 times the average interprobe distance of the assay.

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.