CheckAndFixChrNamesForTransRanges

Check and, if possible, correct the chromosome names in a trans.ranges <code>data.table</code>

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')

CheckAndFixChrNamesForTransRanges function

<dl><dt>trans.ranges</dt>
<dd>A <code><a href="https://rdatatable.gitlab.io/data.table/reference/data.table.html">data.table</a></code> which contains
transcript range and strand information. Please refer to
<code>TranscriptRanges</code> for more details.</dd>
<dt>vcf.df</dt>
<dd>A VCF as a <code>data.frame</code>. Check the names in column
<code>CHROM</code>.</dd>
<dt>ref.genome</dt>
<dd>The reference genome with the chromosome names to check
<code>vcf.df$CHROM</code> against; must be a Bioconductor
<code>BSgenome</code>, e.g.
<code>BSgenome.Hsapiens.UCSC.hg38</code>.</dd>
<dt>name.of.VCF</dt>
<dd>Name of the VCF file.</dd></dl>

Arguments

Check and, if possible, correct the chromosome names in a trans.ranges data.table — CheckAndFixChrNamesForTransRanges

<dl>

<dt>trans.ranges</dt>
<dd>A <code><a href='https://rdatatable.gitlab.io/data.table/reference/data.table.html'>data.table</a></code> which contains
transcript range and strand information. Please refer to
<code>TranscriptRanges</code> for more details.</dd>


<dt>vcf.df</dt>
<dd>A VCF as a <code>data.frame</code>. Check the names in column
<code>CHROM</code>.</dd>


<dt>ref.genome</dt>
<dd>The reference genome with the chromosome names to check
<code>vcf.df$CHROM</code> against; must be a Bioconductor
<code>BSgenome</code>, e.g.
<code>BSgenome.Hsapiens.UCSC.hg38</code>.</dd>


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

</dl>

CheckAndFixChrNamesForTransRanges: Check and, if possible, correct the chromosome names in a trans.ranges `data.table`

Description

Usage

Value

Arguments