CreateOneColSBSMatrix

Create the matrix an SBS catalog for *one* sample from an in-memory VCF.

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')

CreateOneColSBSMatrix function

<dl><dt>vcf</dt>
<dd>An in-memory VCF file annotated with sequence context and
transcript information by function <code>AnnotateSBSVCF</code>. It must
*not* contain indels and must *not* contain DBS (double base
substitutions), or triplet base substitutions etc., even if encoded as
neighboring SBS.</dd>
<dt>sample.id</dt>
<dd>Usually the sample id, but defaults to "count".</dd>
<dt>return.annotated.vcf</dt>
<dd>Whether to return the annotated VCF with
additional columns showing the mutation class for each variant. Default is
FALSE.</dd></dl>

Arguments

Create the matrix an SBS catalog for *one* sample from an in-memory VCF. — CreateOneColSBSMatrix

<dl>

<dt>vcf</dt>
<dd>An in-memory VCF file annotated with sequence context and
transcript information by function <code>AnnotateSBSVCF</code>. It must
*not* contain indels and must *not* contain DBS (double base
substitutions), or triplet base substitutions etc., even if encoded as
neighboring SBS.</dd>


<dt>sample.id</dt>
<dd>Usually the sample id, but defaults to "count".</dd>


<dt>return.annotated.vcf</dt>
<dd>Whether to return the annotated VCF with
additional columns showing the mutation class for each variant. Default is
FALSE.</dd>

</dl>

CreateOneColSBSMatrix: Create the matrix an SBS catalog for one sample from an in-memory VCF.

Description

Usage

Value

Arguments