mutSignatures (version 2.1.1)

chihJenNMF: Perform Non-negative Matrix Factorization using Chih-Jen Lin's Algotithm.

Description

Perform Non-negative Matrix Factorization (alternative approach).

Usage

chihJenNMF(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 a core 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. Chih-Jen Lin original paper: https://ieeexplore.ieee.org/document/4359171/

Examples

# NOT RUN {
x <- mutSignatures:::getTestRunArgs("chihJenNMF")
y <- mutSignatures:::chihJenNMF(v = x$v, r = x$r, params = x$params)
y$w[1:10, ]

# }