getCosmicSignatures

logical, shall signatures be downloaded from a mirror. Set to TRUE if the COSMIC
server goes down.

forceUseMirror

logical, shall data be returned as a mutSignatures-class object. Defaults to TRUE

asMutSign

Obtain latest mutational Signature definitions from COSMIC. FOr more info, please visit: <a href="https://cancer.sanger.ac.uk/cosmic/">https://cancer.sanger.ac.uk/cosmic/</a>

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

getCosmicSignatures function

Obtain latest mutational Signature definitions from COSMIC. FOr more info, please visit: <a href='https://cancer.sanger.ac.uk/cosmic/'>https://cancer.sanger.ac.uk/cosmic/</a>

getCosmicSignatures: Obtain COSMIC mutational Signatures.

Description

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