decipherMutationalProcesses {mutSignatures}

Decipher Mutational Processes Contributing to a Collection of Genomic Mutations.

Description

Decipher Mutational ProCancer cells accumulate DNA mutations as result of DNA damage and DNA repair processes. Thiscomputational framework allows to decipher mutational processes from cancer-derived somatic mutational catalogs.

Usage

decipherMutationalProcesses(input, params)

Arguments

input

a mutationCounts-class object, including a mutation counts data.

params

a mutFrameworkParams-class object including all the parameters required for running the mutational signature analysis.

Details

This is one of the core functions included in the original mutSignatures R library, and in the WTSI MATLAB framework. This is the main user interface for the mutSignatures analysis.

Value

list including all results of the analysis. The extracted signatures (processes) are included in the "processes" element of the list. The relative contribution of each signature in each sample is summarized in the "exposures" element.

Author(s)

Damiano Fantini, [e-mail]

References

More information and examples about mutational signature analysis can be found here:

1. GitHub Repo: https://github.com/dami82/mutSignatures/

2. More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/

3. Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/

4. Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6

5. WTSI framework: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588146/

Examples

library(mutSignatures)
x <- mutSignatures:::getTestRunArgs("decipherMutationalProcesses")
x$muts
y <- mutSignatures::decipherMutationalProcesses(input = x$muts, 
                                                params = x$params)
y$Results$signatures