get.toptn

Generate a tri-nucleotide summary for each sliding window

Kataegis is a localized hypermutation occurring when a region is enriched in somatic SNVs. Kataegis can result from multiple cytosine deaminations catalyzed by the AID/APOBEC family of proteins. This package contains functions to detect kataegis from SNVs in BED format. This package reports two scores per kataegic event, a hypermutation score and an APOBEC mediated kataegic score. Yousif, F. et al.; The Origins and Consequences of Localized and Global Somatic Hypermutation; Biorxiv 2018 <doi:10.1101/287839>.

Paul Boutros

SeqKat

Detection of Kataegis

Fouad Yousif

Xihui Lin

Fan Fan

Christopher Lalansingh

John Macdonald

Paul C. Boutros

get.toptn function

<dl><dt>somatic.subset</dt>
<dd>Data frame of somatic variants subset for a specific chromosome</dd>
<dt>chr</dt>
<dd>Chromosome</dd>
<dt>start.bp</dt>
<dd>Starting position</dd>
<dt>end.bp</dt>
<dd>Ending position</dd>
<dt>ref.dir</dt>
<dd>Path to a directory containing the reference genome.</dd></dl>

Arguments

Author

Get Top Trinucleotides — get.toptn

<dl>

<dt>somatic.subset</dt>
<dd>Data frame of somatic variants subset for a specific chromosome</dd>


<dt>chr</dt>
<dd>Chromosome</dd>


<dt>start.bp</dt>
<dd>Starting position</dd>


<dt>end.bp</dt>
<dd>Ending position</dd>


<dt>ref.dir</dt>
<dd>Path to a directory containing the reference genome.</dd>

</dl>

get.toptn: Get Top Trinucleotides

Description

Usage

Arguments

Author

Examples