SplitSBSVCF

SBSs are single base substitutions,
e.g. C&gt;T, A&gt;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')

SplitSBSVCF function

<dl><dt>vcf.df</dt>
<dd>An in-memory data frame containing an SBS VCF file contents.</dd>
<dt>max.vaf.diff</dt>
<dd>The maximum difference of VAF, default value is 0.02. If
the absolute difference of VAFs for adjacent SBSs is bigger than
<code>max.vaf.diff</code>, then these adjacent SBSs are likely to be "merely"
asynchronous single base mutations, opposed to a simultaneous doublet
mutation or variants involving more than two consecutive bases.</dd>
<dt>name.of.VCF</dt>
<dd>Name of the VCF file.</dd></dl>

Arguments

Split an in-memory SBS VCF into pure SBSs, pure DBSs, and variants involving
&gt; 2 consecutive bases — SplitSBSVCF

<dl>

<dt>vcf.df</dt>
<dd>An in-memory data frame containing an SBS VCF file contents.</dd>


<dt>max.vaf.diff</dt>
<dd>The maximum difference of VAF, default value is 0.02. If
the absolute difference of VAFs for adjacent SBSs is bigger than
<code>max.vaf.diff</code>, then these adjacent SBSs are likely to be "merely"
asynchronous single base mutations, opposed to a simultaneous doublet
mutation or variants involving more than two consecutive bases.</dd>


<dt>name.of.VCF</dt>
<dd>Name of the VCF file.</dd>

</dl>

SplitSBSVCF: Split an in-memory SBS VCF into pure SBSs, pure DBSs, and variants involving > 2 consecutive bases

Description

Usage

Value

Arguments