mutSignatures (version 2.1.1)

alexaNMF: Perform Non-negative Matrix Factorization using Brunet's Algotithm.

Description

Perform Non-negative Matrix Factorization.

Usage

alexaNMF(v, r, params)

Arguments

v

numeric matrix of Mutation Type Counts

r

numeric, number of signatures to extract

params

list including all paramaters for running the analysis

Value

list including all paramaters for running the analysis:

1. W extracted signatures

2. H contribution of each signature in all the samples of the input mut count matrix

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("alexaNMF")
y <- mutSignatures:::alexaNMF(v = x$v, r = x$r, params = x$params)
y$w[1:5, ]

# }