msigPlot

msigPlot,mutationSignatures-method

msigPlot,mutationCounts-method

msigPlot,mutSignExposures-method

<p>additional parameters, including standard graphical parameters, as well as 
a set of class-specific arguments:
* x is a mutationSignatures object: 
    - signature, numeric; numeric index of the signature to display
    - main, string; title of the plot
* x is a mutationCounts object
    - sample, numeric or string, i.e. the identifier or the index of the sample to be plotted
    - main, string, title of the plot
 * x is a mutSignExposures object
    - top, integer, the maximum number of samples to be plotted</p>

<p>Generate standard plots using data from mutsignature-class objects.</p>

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>.

msigPlot: Method msigPlot.

Description

Usage

Arguments