chihJenNMF {mutSignatures} | R Documentation |
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:
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W extracted signatures
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H contribution of each signature in all the samples of the input mut count matrix
Author(s)
Damiano Fantini, damiano.fantini@gmail.com
References
More information and examples about mutational signature analysis can be found here:
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GitHub Repo: https://github.com/dami82/mutSignatures/
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More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/
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Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/
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Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6
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Chih-Jen Lin original paper: https://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, ]