mutationCounts-class

initialize,mutationCounts-method

the mutationCounts object being built

.Object

data.frame including mutation count values for each biological sample

data.frame including information about mutation types

muts

data.frame including information about sample identifiers (unique names)

samples

Class mutationCounts defines objects storing Mutation COunts data.

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

mutationCounts-class function

<dl class="dl-horizontal">
<dt><code>counts</code></dt><dd>data.frame including information about mutation counts</dd></dl><dt><code>mutTypes</code></dt><dd>data.frame including information about mutation types</dd><dt><code>sampleId</code></dt><dd>data.frame including information about sample identifiers</dd>

mutationCounts-class: Class mutationCounts.

Description

Usage

Arguments

Slots