custom_cssls

Pset

<p>This function contributes to solving a nonnegative least square linear 
problem using normal equations and the fast combinatorial strategy from Van 
Benthem et al. (2004). This implementation is similar to that included in the
NMF R package by Renaud Gaujoux and Cathal Seoighe, 
and it is tailored to the data used in the mutational signature analysis. 
For more info, see: <a href="https://CRAN.R-project.org/package=NMF">https://CRAN.R-project.org/package=NMF</a></p>

internal

Cancer cells accumulate DNA mutations as result of DNA damage and DNA repair processes. This computational framework is aimed at deciphering DNA mutational signatures operating in cancer. The framework includes modules that support raw data import and processing, mutational signature extraction, and results interpretation and visualization. The framework accepts widely used file formats storing information about DNA variants, such as Variant Call Format files. The framework performs Non-Negative Matrix Factorization to extract mutational signatures explaining the observed set of DNA mutations. Bootstrapping is performed as part of the analysis. The framework supports parallelization and is optimized for use on multi-core systems. The software was described by Fantini D et al (2020) <doi:10.1038/s41598-020-75062-0> and is based on a custom R-based implementation of the original MATLAB WTSI framework by Alexandrov LB et al (2013) <doi:10.1016/j.celrep.2012.12.008>.

Damiano Fantini

mutSignatures

Decipher Mutational Signatures from Somatic Mutational Catalogs

custom_cssls function

<p>This function contributes to solving a nonnegative least square linear 
problem using normal equations and the fast combinatorial strategy from Van 
Benthem et al. (2004). This implementation is similar to that included in the
NMF R package by Renaud Gaujoux and Cathal Seoighe, 
and it is tailored to the data used in the mutational signature analysis. 
For more info, see: <a href='https://CRAN.R-project.org/package=NMF'>https://CRAN.R-project.org/package=NMF</a></p>

custom_cssls: Custom CSSLS.

Description

Usage

Arguments

Value

Examples