chihJenNMF: Perform Non-negative Matrix Factorization using Chih-Jen...

In dami82/mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

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

Details

This is a core internal function.

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

Author(s)

Damiano Fantini, [e-mail]

References

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

1. Official website: http://www.mutsignatures.org

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

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

4. Chih-Jen Lin original paper: http://ieeexplore.ieee.org/document/4359171/

Examples

x <- mutSignatures:::getTestRunArgs("chihJenNMF")
y <- mutSignatures:::chihJenNMF(v = x$v, r = x$r, params = x$params)
y$w[1:10, ]

dami82/mutSignatures documentation built on Jan. 24, 2023, 12:21 a.m.