handle_hyper_mutation

<p>a <code>matrix</code> used for NMF decomposition with rows indicate samples and columns indicate components.</p>

nmf_matrix

<p>This can be used for SNV/INDEL count matrix. For copy number analysis,
please skip it.</p>

Genomic alterations including single nucleotide
substitution, copy number alteration, etc. are the major force for
cancer initialization and development. Due to the specificity of
molecular lesions caused by genomic alterations, we can generate
characteristic alteration spectra, called 'signature' (Wang, Shixiang,
et al.  (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil
B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff,
et al. (2018) <DOI:10.1038/s41588-018-0179-8>).  This package helps
users to extract, analyze and visualize signatures from genomic
alteration records, thus providing new insight into cancer study.

Shixiang Wang

sigminer

Extract, Analyze and Visualize Signatures for Genomic Variations

Xue-Song Liu

Tao Wu

Ziyu Tao

Geoffrey Macintyre

Anand Mayakonda

handle_hyper_mutation function

Handle Hypermutant Samples — handle_hyper_mutation

Handle Hypermutant Samples

handle_hyper_mutation: Handle Hypermutant Samples

Description

Usage

Arguments

Value

References