getReferenceSignatures: getReferenceSignatures

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

getReferenceSignatures

Description

This function returns the reference signatures for a given mutation type as defined in Degasperi et al. 2020 Nat Cancer paper, and Degasperi et al. 2022 Science paper.

Usage

getReferenceSignatures(version = "latest", typemut = "subs", verbose = TRUE)

Arguments

version	version "1" includes subs or rearr (ICGC cohort) reference signatures from Degasperi et al. 2020, while version "2" includes the improved subs reference signatures and the DNV signatures from Degasperi et al. 2022. Set to "latest" to get the latest signature available for a given mutation type.
typemut	either subs, DNV or rearr

Value

reference signatures matrix

References

A. Degasperi, T. D. Amarante, J. Czarnecki, S. Shooter, X. Zou, D. Glodzik, S. Morganella, A. S. Nanda, C. Badja, G. Koh, S. E. Momen, I. Georgakopoulos-Soares, J. M. L. Dias, J. Young, Y. Memari, H. Davies, S. Nik-Zainal. A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies, Nature Cancer, https://doi.org/10.1038/s43018-020-0027-5, 2020.

A. Degasperi, X. Zou, T. D. Amarante, ..., H. Davies, Genomics England Research Consortium, S. Nik-Zainal. Substitution mutational signatures in whole-genome-sequenced cancers in the UK population. Science, 2022.

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