mutSignatures (version 2.1.1)

deconvoluteMutCounts: Deconvolute Mutation Counts.

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

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

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.

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

# NOT RUN {
 
x <- mutSignatures:::getTestRunArgs("deconvoluteMutCounts")
y <- mutSignatures:::deconvoluteMutCounts(input_mutCounts = as.matrix(x$muts),
                                          params = as.list(x$params))
y$processes[1:10,]


# }