fitSignaturesWithSignatures: fitSignaturesWithSignatures

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

fitSignaturesWithSignatures

Description

This function attempts to reconstruct a set of signatures (signatures_to_fit) using a second set of signatures (signatures_to use), either just checking the similarity between the signatures of the first and the second set, or using a linear combination of signatures in the second set to model the first set. The typical use of this function would be to check whether a set of extracted signatures can be matched to a set of known signatures, a procedure often called signature assignment or signature identification.

Usage

fitSignaturesWithSignatures(
  signatures_to_fit,
  signatures_to_use,
  max_combinations = 2,
  sig_min_contrib = 0.15,
  minsim = 0.75,
  max_from_each_class = 10,
  nparallel = 1
)

Arguments

signatures_to_fit	matrix with the mutational signatures that need to be identified/fitted. Each column has a signature and each row corresponds to a mutational channel. Columns need to sum to 1.
signatures_to_use	matrix of mutational signatures to be used as a reference and that will be fitted/combined to match the signatures_to_fit. Each column has a signature and each row corresponds to a mutational channel. Columns need to sum to 1.
max_combinations	maximum number of signatures_to_use to be used as a linear combination to fit each signatures_to_fit
sig_min_contrib	minimum percentage of contribution that a signatures_to_use should have to a linear combination when matching a signature in signatures_to_fit
minsim	minimum cosine similarity between a signatures_to_fit and a match, where a match is either a signature in signatures_to_use or a linear combination of signatures in signatures_to_use
max_from_each_class	maximum number of matches to consider in each class, where the class indicates the number of signatures in a linear combination. If there are more matches in the class than the maximum specified, then the matches with the highest cosine similarity will be reported
nparallel	how many parallel cpus to use

Value

tables with the best linear combinations of signatures in signatures_to_use that match signatures in signatures_to_fit

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