get.trinucleotide.counts

Aggregates the total counts of each possible trinucleotide.

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.trinucleotide.counts function

<dl><dt>ref.dir</dt>
<dd>Path to a directory containing the reference genome.</dd>
<dt>ref.name</dt>
<dd>Name of the reference genome being used (i.e. hg19, GRCh38, etc)</dd>
<dt>output.dir</dt>
<dd>Path to a directory where output will be created.</dd></dl>

Arguments

Author

Get Trinucleotide Counts — get.trinucleotide.counts

<dl>

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


<dt>ref.name</dt>
<dd>Name of the reference genome being used (i.e. hg19, GRCh38, etc)</dd>


<dt>output.dir</dt>
<dd>Path to a directory where output will be created.</dd>

</dl>

get.trinucleotide.counts: Get Trinucleotide Counts

Description

Usage

Arguments

Author

Examples