convertExposuresFromOrganToRefSigsIfAny: convertExposuresFromOrganToRefSigsIfAny

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

convertExposuresFromOrganToRefSigsIfAny

Description

This function inspects an exposure matrix, and converts organ-specific signature exposures into reference signature exposures if it finds any. If the exposure matrix contains reference signature exposures to start with, then reference signature exposures are merged if possible. The function will detect the version of the signatures automatically.

Usage

convertExposuresFromOrganToRefSigsIfAny(expMatrix, typemut = "subs")

Arguments

expMatrix	exposures matrix obatined from fitting organ-specific signatures
typemut	either subs, DNV or rearr

Value

exposure matrix with converted signatures, or unaltered exposure matrix if organ-specific signatures where not found

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.

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