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" catalogs
of mutational spectra or signatures.

In-Depth Characterization and Analysis of Mutational Signatures
('ICAMS')

package-ubuntu-20.04-r-4.0.5#cran#ICAMS-2.3.10

<p>Read chromosome and position information from a bed format file.
</p>

<table summary="R argblock"><tr valign="top">
<td><code>file</code></td>
<td>
<p>Path to the file in bed format.</p>
</td>
</tr></table>

<p>A data.table keyed by chrom, start, and end. It uses one-based
coordinates.
</p>

package-ubuntu-20.04-r-4.0.5#cran#ICAMS-2.3.10#docs#ReadBedRanges

ReadBedRanges

Description

Usage

Arguments

Value

ICAMS

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