ReadStrelkaSBSVCFs

Read Strelka SBS (single base substitutions) VCF files.

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')

ReadStrelkaSBSVCFs function

<dl><dt>files</dt>
<dd>Character vector of file paths to the VCF files.</dd>
<dt>names.of.VCFs</dt>
<dd>Character vector of names of the VCF files. The order of
names in <code>names.of.VCFs</code> should match the order of VCF file paths in
<code>files</code>. If <code>NULL</code>(default), this function will remove all of the
path up to and including the last path separator (if any) in <code>files</code>
and file paths without extensions (and the leading dot) will be used as the
names of the VCF files.</dd></dl>

Arguments

Read Strelka SBS (single base substitutions) VCF files. — ReadStrelkaSBSVCFs

<dl>

<dt>files</dt>
<dd>Character vector of file paths to the VCF files.</dd>


<dt>names.of.VCFs</dt>
<dd>Character vector of names of the VCF files. The order of
names in <code>names.of.VCFs</code> should match the order of VCF file paths in
<code>files</code>. If <code>NULL</code>(default), this function will remove all of the
path up to and including the last path separator (if any) in <code>files</code>
and file paths without extensions (and the leading dot) will be used as the
names of the VCF files.</dd>

</dl>

ReadStrelkaSBSVCFs: Read Strelka SBS (single base substitutions) VCF files.

Description

Usage

Value

Arguments