PlasmaMutationDetector: Tumor Mutation Detection in Plasma

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.

Author
Yves Rozenholc, Nicolas P├ęcuchet, Pierre Laurent-Puig
Date of publication
2016-09-09 10:13:42
Maintainer
Yves Rozenholc <yves.rozenholc@parisdescartes.fr>
License
MIT + file LICENSE
Version
1.5.2

View on CRAN

Man pages

background_error_rate
The package provide the SNV and INDEL PERs computed for the...
BuildCtrlErrorRate
function BuildCtrlErrorRate
DetectPlasmaMutation
function DetectPlasmaMutation
hotspot
The package provide a list of known hotspot positions located...
MAF_from_BAM
function MAF_from_BAM
positions_ranges
The package provide the positions and ranges computed for the...
PrepareLibrary
function PrepareLibrary

Files in this package

PlasmaMutationDetector
PlasmaMutationDetector/inst
PlasmaMutationDetector/inst/extdata
PlasmaMutationDetector/inst/extdata/4test_only
PlasmaMutationDetector/inst/extdata/4test_only/case
PlasmaMutationDetector/inst/extdata/4test_only/case/rBAM
PlasmaMutationDetector/inst/extdata/4test_only/case/rBAM/case1.chr7.bam
PlasmaMutationDetector/inst/extdata/4test_only/case/rBAM/case1.chr7.bam.bai
PlasmaMutationDetector/inst/extdata/4test_only/case/BER
PlasmaMutationDetector/inst/extdata/4test_only/case/BER/case1.chr7_MAF.txt
PlasmaMutationDetector/inst/extdata/4test_only/ctrl
PlasmaMutationDetector/inst/extdata/4test_only/ctrl/rBAM
PlasmaMutationDetector/inst/extdata/4test_only/ctrl/rBAM/ctrl1-downsample-05.bam.bai
PlasmaMutationDetector/inst/extdata/4test_only/ctrl/rBAM/ctrl1-downsample-05.bam
PlasmaMutationDetector/inst/extdata/4test_only/ctrl/BER
PlasmaMutationDetector/inst/extdata/4test_only/ctrl/BER/ctrl1-downsample-05_MAF.txt.zip
PlasmaMutationDetector/inst/extdata/Info
PlasmaMutationDetector/inst/extdata/Info/lungcolonV2.bed.txt
PlasmaMutationDetector/NAMESPACE
PlasmaMutationDetector/data
PlasmaMutationDetector/data/positions_ranges.rda
PlasmaMutationDetector/data/hotspot.txt.gz
PlasmaMutationDetector/data/background_error_rate.txt.gz
PlasmaMutationDetector/R
PlasmaMutationDetector/R/functions.R
PlasmaMutationDetector/MD5
PlasmaMutationDetector/DESCRIPTION
PlasmaMutationDetector/man
PlasmaMutationDetector/man/positions_ranges.Rd
PlasmaMutationDetector/man/MAF_from_BAM.Rd
PlasmaMutationDetector/man/background_error_rate.Rd
PlasmaMutationDetector/man/hotspot.Rd
PlasmaMutationDetector/man/DetectPlasmaMutation.Rd
PlasmaMutationDetector/man/BuildCtrlErrorRate.Rd
PlasmaMutationDetector/man/PrepareLibrary.Rd
PlasmaMutationDetector/LICENSE