makeReferenceCN: Generate reference distribution from copy number data

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

Generate reference distribution from copy number data

Description

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

Usage

makeReferenceCN(
  segmentTable,
  pairs,
  patients = NULL,
  delimiter = 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. 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 (optional).
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.

Details

The default is to assume one tumour pair per patient. If the sample is found in more than one pair, indicating more than one pair per patient, an error will be thrown. In that case you must specify either patients or delimiter.

Value

A numeric vector of pair scores comprising the reference distribution.

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