assignSignatureProbabilityToMutations: Assign Signature Probability to Mutations

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

Assign Signature Probability to Mutations

Description

Given an annotated set of mutations and an exposure matrix from signature fit, this function estimates the probability that each mutation generates from each signature.

Usage

assignSignatureProbabilityToMutations(
  sampleMutations,
  sampleSigsExposures,
  signatures,
  catalogue = NULL,
  enableUnassigned = FALSE,
  verbose = TRUE
)

Arguments

sampleMutations	list of annotated mutations obtained usually after building catalogues, for example using the functions vcfToSNVcatalogues or bedpeToRearrCatalogues
sampleSigsExposures	matrix of exposures with only one row (one sample) and the exposures for each signature as columns
signatures	mutational signatures matrix with the signatures used during signature fitting
catalogue	sample catalogue, used only if enableUnassigned is true
enableUnassigned	if true, probability can be assigned to an unassigned category, rather than a signature. This can lead to structural variants that are classified as unassigned. In practice, the positive part of the difference between catalogue and reconstruction is used as the unassigned signature and the unassigned exposures are also used.

Value

matrix of mutations with an additional column containing the probabilities in a text format that can be expanded into a matrix using expandColumnToMatrix

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.