handle_hyper_mutation

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

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. (2021)
<DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al.
(2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher D., et al.
(2022) <DOI:10.1038/s41586-022-04738-6>). 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 Mutational Signatures for Genomic
Variations

Ziyu Tao

Huimin Li

Tao Wu

Xue-Song Liu

Anand Mayakonda

handle_hyper_mutation function

<dl><dt>nmf_matrix</dt>
<dd>a <code>matrix</code> used for NMF decomposition with rows indicate samples and columns indicate components.</dd></dl>

Arguments

Handle Hypermutant Samples — handle_hyper_mutation

<dl>

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

</dl>

handle_hyper_mutation: Handle Hypermutant Samples

Description

Usage

Value

Arguments

References