getOrganSignatures: getOrganSignatures

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

getOrganSignatures

Description

This function returns the organ-specific signatures for a given organ and mutation type as defined in Degasperi et al. 2020 Nat Cancer paper.

Usage

getOrganSignatures(
  organ,
  version = "latest",
  cohort = "best",
  typemut = "subs",
  verbose = FALSE
)

Arguments

organ	one of the following: "Biliary", "Bladder", "Bone_SoftTissue", "Breast", "Cervix", "CNS", "Colorectal", "Esophagus", "Head_neck", "Kidney", "Liver", "Lung", "Lymphoid", "Ovary", "Pancreas", "Prostate", "Skin", "Stomach", "Uterus"
version	version "1" includes subs or rearr (ICGC cohort) organ-specific signatures from Degasperi et al. 2020, while version "2" includes the improved subs organ-specific signatures from ICGC as well as Hartwig and GEL, and the new DNV signatures. Set to "latest" to get the latest signature available for a given mutation type.
cohort	for version 1 signatures only ICGC cohort is available, while for version 2 signatures ICGC, Hartwig and GEL cohort can be requested. Use "best" to get the most appropriate cohort for a given organ.
typemut	either subs, DNV or rearr

Value

organ-specific 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.

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