SplitListOfStrelkaSBSVCFs

SBSs are single base substitutions,
e.g. C&gt;T, A&lt;G,.... DBSs are double base substitutions,
e.g. CC&gt;TT, AT&gt;GG, ... Variants involving &gt; 2 consecutive
bases are rare, so this function just records them. These
would be variants such ATG&gt;CCT, AGAT&gt;TCTA, ...

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')

SplitListOfStrelkaSBSVCFs function

<dl><dt>list.of.vcfs</dt>
<dd>A list of in-memory data frames containing Strelka SBS
VCF file contents.</dd>
<dt>suppress.discarded.variants.warnings</dt>
<dd>Logical. Whether to suppress
warning messages showing information about the discarded variants. Default
is TRUE.</dd></dl>

Arguments

Split a list of in-memory Strelka SBS VCF into SBS, DBS, and variants involving
&gt; 2 consecutive bases — SplitListOfStrelkaSBSVCFs

<dl>

<dt>list.of.vcfs</dt>
<dd>A list of in-memory data frames containing Strelka SBS
VCF file contents.</dd>


<dt>suppress.discarded.variants.warnings</dt>
<dd>Logical. Whether to suppress
warning messages showing information about the discarded variants. Default
is TRUE.</dd>

</dl>

SplitListOfStrelkaSBSVCFs: Split a list of in-memory Strelka SBS VCF into SBS, DBS, and variants involving > 2 consecutive bases

Description

Usage

Value

Arguments