positions_ranges

positions_ranges.rda

pos_ind

pos_snp

pos_ranges

This file contains 4 variables<ul>
<li><code>pos_ind</code>, vector of chars, of the form chrN:XXXXXXXXX defining genomic positions of the Ion AmpliSeq&lt;U+2122&gt; Colon and Lung Cancer Panel v2</li>
<li><code>pos_snp</code>, vector of chars, of the form chrN:XXXXXXXXX defining the known snp genomic positions</li>
<li><code>pos_ranges</code>, GRanges object, describing the 92 amplicons of the Ion AmpliSeq&lt;U+2122&gt; Colon and Lung Cancer Panel v2</li>
</ul>

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

positions_ranges function

The package provide the positions and ranges computed for the Ion AmpliSeq&lt;U+2122&gt; Colon and Lung Cancer Panel v2 as a Rdata file <code>positions_ranges.rda</code>. — positions_ranges

The package provide the positions and ranges computed for the Ion AmpliSeq&lt;U+2122&gt; Colon and Lung Cancer Panel v2 as a Rdata file <code>positions_ranges.rda</code>.

positions_ranges: The package provide the positions and ranges computed for the Ion AmpliSeq<U+2122> Colon and Lung Cancer Panel v2 as a Rdata file `positions_ranges.rda`.

Description

Usage

Arguments

References

See Also