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PlasmaMutationDetector2 (version 1.1.11)

Tumor Mutation Detection in Plasma using Barcoding

Description

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, Bjrnar Gilje, Herish Garresori, Satu Oltedal, Rakel Brendsdal Forthun, Anders Molven, Yves Rozenholc and Oddmund N\o{o}rdgaard (2022) .

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Install

install.packages('PlasmaMutationDetector2')

Monthly Downloads

15

Version

1.1.11

License

MIT + file LICENSE

Maintainer

Yves Rozenholc

Last Published

May 3rd, 2022

Functions in PlasmaMutationDetector2 (1.1.11)

hotspot

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

function PrepareLibrary
DetectPlasmaMutation

function DetectPlasmaMutation
BuildCtrlErrorRate

function BuildCtrlErrorRate
MAF_from_BAM

function MAF_from_BAM
LoadBackgroundErrorRate

function LoadBackgroundErrorRate
background_error_rate

The package provide the SNV and INDEL PERs computed for the Ion AmpliSeq<U+2122> Colon and Lung Cancer Panel v2 from 29 controls in a table available in the data file background_error_rate.txt.
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.