CheckAndReturnIDMatrix

Check and return the ID mutation matrix

internal

Analysis and visualization of experimentally elucidated mutational
signatures -- the kind of analysis and visualization in Boot et al.,
"In-depth characterization of the cisplatin mutational signature in
human cell lines and in esophageal and liver tumors", Genome Research 2018,
<doi:10.1101/gr.230219.117> and
"Characterization of colibactin-associated mutational signature in an
Asian oral squamous cell carcinoma and in other mucosal tumor types",
Genome Research 2020 <doi:10.1101/gr.255620.119>.
'ICAMS' stands for In-depth Characterization
and Analysis of Mutational Signatures. 'ICAMS' has functions to read in
variant call files (VCFs) and to collate the corresponding catalogs of
mutational spectra and to analyze and plot catalogs of mutational spectra
and signatures. Handles both "counts-based" and "density-based" (i.e.
representation as mutations per megabase) mutational spectra or signatures.

Steve Rozen

ICAMS

In-Depth Characterization and Analysis of Mutational Signatures
('ICAMS')

CheckAndReturnIDMatrix function

<dl><dt>annotated.vcf</dt>
<dd>An annotated ID VCF with additional column
<code>ID.class</code> showing ID classification for each variant.</dd>
<dt>discarded.variants</dt>
<dd>A <code>data.frame</code> which contains rows of ID
variants which are excluded in the analysis.</dd>
<dt>ID.mat</dt>
<dd>The ID mutation count matrix.</dd>
<dt>return.annotated.vcf</dt>
<dd>Whether to return <code>annotated.vcf</code>. Default is
FALSE.</dd></dl>

Arguments

Check and return the ID mutation matrix — CheckAndReturnIDMatrix

<dl>

<dt>annotated.vcf</dt>
<dd>An annotated ID VCF with additional column
<code>ID.class</code> showing ID classification for each variant.</dd>


<dt>discarded.variants</dt>
<dd>A <code>data.frame</code> which contains rows of ID
variants which are excluded in the analysis.</dd>


<dt>ID.mat</dt>
<dd>The ID mutation count matrix.</dd>


<dt>return.annotated.vcf</dt>
<dd>Whether to return <code>annotated.vcf</code>. Default is
FALSE.</dd>

</dl>

CheckAndReturnIDMatrix: Check and return the ID mutation matrix

Description

Usage

Value

Arguments