Package: PlasmaMutationDetector2 1.1.11
Rozenholc
PlasmaMutationDetector2: Tumor Mutation Detection in Plasma using Barcoding
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, Bjørnar 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>.
Authors:
PlasmaMutationDetector2_1.1.11.tar.gz
PlasmaMutationDetector2_1.1.11.zip(r-4.5)PlasmaMutationDetector2_1.1.11.zip(r-4.4)
PlasmaMutationDetector2_1.1.11.tgz(r-4.5-any)PlasmaMutationDetector2_1.1.11.tgz(r-4.4-any)
PlasmaMutationDetector2_1.1.11.tar.gz(r-4.5-noble)PlasmaMutationDetector2_1.1.11.tar.gz(r-4.4-noble)
PlasmaMutationDetector2_1.1.11.tgz(r-4.4-emscripten)PlasmaMutationDetector2_1.1.11.tgz(r-4.3-emscripten)
PlasmaMutationDetector2.pdf |PlasmaMutationDetector2.html✨
PlasmaMutationDetector2/json (API)
| # Install 'PlasmaMutationDetector2' in R: |
| install.packages('PlasmaMutationDetector2', repos = c('https://cranhaven.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cranhaven/cranhaven.r-universe.dev/issues
- background_error_rate - The package provide the SNV and INDEL PERs computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 from 29 controls in a table available in the data file 'background_error_rate.txt'.
- hotspot - The package provide a list of known hotspot positions located on the amplicons of the Ion AmpliSeq™ 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.
- pos_ind - The package provide the positions and ranges computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a Rdata file 'positions_ranges.rda'.
- pos_ranges - The package provide the positions and ranges computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a Rdata file 'positions_ranges.rda'.
- pos_snp - The package provide the positions and ranges computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a Rdata file 'positions_ranges.rda'.
Last updated 18 days agofrom:dbefabb5ae (on package/PlasmaMutationDetector2). Checks:1 OK, 5 NOTE. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 02 2025 |
| R-4.5-win | NOTE | Feb 02 2025 |
| R-4.5-mac | NOTE | Feb 02 2025 |
| R-4.5-linux | NOTE | Feb 02 2025 |
| R-4.4-win | NOTE | Feb 02 2025 |
| R-4.4-mac | NOTE | Feb 02 2025 |
Exports:BuildCtrlErrorRateDetectPlasmaMutationLoadBackgroundErrorRateMAF_from_BAMPrepareLibrary
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArrayDEoptimRfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangrobustbaseRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The package provide the SNV and INDEL PERs computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 from 29 controls in a table available in the data file 'background_error_rate.txt'. | background_error_rate background_error_rate.txt |
| function BuildCtrlErrorRate | BuildCtrlErrorRate |
| function DetectPlasmaMutation | DetectPlasmaMutation |
| The package provide a list of known hotspot positions located on the amplicons of the Ion AmpliSeq™ 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. | hotspot hotspot.txt |
| function LoadBackgroundErrorRate | LoadBackgroundErrorRate |
| function MAF_from_BAM | MAF_from_BAM |
| The package provide the positions and ranges computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a Rdata file 'positions_ranges.rda'. | positions_ranges positions_ranges.rda pos_ind pos_ranges pos_snp |
| function PrepareLibrary | PrepareLibrary |
