hotspot

hotspot.txt

<p>The package provide a list of known hotspot positions located on the amplicons of the Ion AmpliSeq&lt;U+2122&gt; Colon and Lung Cancer Panel v2 as a txt file <code>hotspot.txt</code> which contains a vector/variable ---named chrpos (first row)--- of chars, of the form chrN:XXXXXXXXX defining genomic positions.</p>

data

Aims at detecting single nucleotide variation
(SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used
as a surrogate marker for tumor, at each base position of an Next Generation
Sequencing (NGS) analysis using barcoding. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples.
This package has been used for Kjersti Tjensvoll, Morten Lapin, Bj<c3><b8>rnar Gilje, Herish Garresori, Satu Oltedal, Rakel Brendsdal Forthun, Anders Molven, Yves Rozenholc and Oddmund N\o{o}rdgaard (2022) <https://www.nature.com/articles/s41598-022-09698-5>.

Yves Rozenholc

PlasmaMutationDetector2

Tumor Mutation Detection in Plasma using Barcoding

hotspot function

The package provide a list of known hotspot positions located on the amplicons of the Ion AmpliSeq&lt;U+2122&gt; Colon and Lung Cancer Panel v2 as a txt file <code>hotspot.txt</code> which contains a vector/variable ---named chrpos (first row)--- of chars, of the form chrN:XXXXXXXXX defining genomic positions. — hotspot

The package provide a list of known hotspot positions located on the amplicons of the Ion AmpliSeq&lt;U+2122&gt; Colon and Lung Cancer Panel v2 as a txt file <code>hotspot.txt</code> which contains a vector/variable ---named chrpos (first row)--- of chars, of the form chrN:XXXXXXXXX defining genomic positions.

Description

Usage

Arguments

References