GetCustomKmerCounts

Generate custom k-mer abundance from a given reference genome

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')

GetCustomKmerCounts function

<dl><dt>k</dt>
<dd>Length of k-mers (k&gt;=2)</dd>
<dt>ref.genome</dt>
<dd>A <code>ref.genome</code> argument as described in
<code>ICAMS</code>.</dd>
<dt>custom.ranges</dt>
<dd>A keyed data table which has custom ranges information. It
has three columns: chrom, start and end. It should use one-based coordinate
system. You can use the internal function in this package
<code>ICAMS:::ReadBedRanges</code> to read a BED file in 0-based coordinates and
convert it to 1-based coordinates.</dd>
<dt>filter.path</dt>
<dd>If given, homopolymers will be masked from
genome(sequence). Only simple repeat masking is accepted now.</dd>
<dt>verbose</dt>
<dd>If <code>TRUE</code> generate progress messages.</dd></dl>

Arguments

Generate custom k-mer abundance from a given reference genome — GetCustomKmerCounts

<dl>

<dt>k</dt>
<dd>Length of k-mers (k&gt;=2)</dd>


<dt>ref.genome</dt>
<dd>A <code>ref.genome</code> argument as described in
<code>ICAMS</code>.</dd>


<dt>custom.ranges</dt>
<dd>A keyed data table which has custom ranges information. It
has three columns: chrom, start and end. It should use one-based coordinate
system. You can use the internal function in this package
<code>ICAMS:::ReadBedRanges</code> to read a BED file in 0-based coordinates and
convert it to 1-based coordinates.</dd>


<dt>filter.path</dt>
<dd>If given, homopolymers will be masked from
genome(sequence). Only simple repeat masking is accepted now.</dd>


<dt>verbose</dt>
<dd>If <code>TRUE</code> generate progress messages.</dd>

</dl>

GetCustomKmerCounts: Generate custom k-mer abundance from a given reference genome

Description

Usage

Value

Arguments