deconvoluteMutCounts: Deconvolute Mutation Counts.

In mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

Description

Characterize mutational signatures from cancer-derived somatic mutational catalogs.

Usage

deconvoluteMutCounts(input_mutCounts, params)

Arguments

input_mutCounts	numeric matrix of Mutation Type Counts
params	list including all parameters required for running the analysis

Details

This is one of the core functions included in the original mutSignatures R library, and in the WTSI MATLAB framework. This is an internal function.

Value

list including all the results from the deconvolution analysis. This function is called within thedecipherMutationalProcesses() function after parameters and input data have been validated

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

 
x <- mutSignatures:::getTestRunArgs("deconvoluteMutCounts")
y <- mutSignatures:::deconvoluteMutCounts(input_mutCounts = as.matrix(x$muts),
                                          params = as.list(x$params))
y$processes[1:10,]

mutSignatures documentation built on Nov. 9, 2020, 9:06 a.m.