PlasmaMutationDetector (version 1.7.2)

Tumor Mutation Detection in Plasma

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. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples.

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Version

Install

install.packages('PlasmaMutationDetector')

Monthly Downloads

181

Version

1.7.2

License

MIT + file LICENSE

Maintainer

Yves Rozenholc

Last Published

June 11th, 2018

Functions in PlasmaMutationDetector (1.7.2)

PrepareLibrary

function PrepareLibrary

LoadBackgroundErrorRate

function LoadBackgroundErrorRate

BuildCtrlErrorRate

function BuildCtrlErrorRate

MAF_from_BAM

function MAF_from_BAM

DetectPlasmaMutation

function DetectPlasmaMutation

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.

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.