Package: PlasmaMutationDetector 1.7.2
Yves Rozenholc
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.
Authors:
PlasmaMutationDetector_1.7.2.tar.gz
PlasmaMutationDetector_1.7.2.tar.gz(r-4.5-noble)PlasmaMutationDetector_1.7.2.tar.gz(r-4.4-noble)
PlasmaMutationDetector_1.7.2.tgz(r-4.4-emscripten)PlasmaMutationDetector_1.7.2.tgz(r-4.3-emscripten)
PlasmaMutationDetector.pdf |PlasmaMutationDetector.html✨
PlasmaMutationDetector/json (API)
# Install 'PlasmaMutationDetector' in R: |
install.packages('PlasmaMutationDetector', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- 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'.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 7 years agofrom:9a5b641f80. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 15 2024 |
R-4.5-linux | OK | Dec 15 2024 |
Exports:BuildCtrlErrorRateDetectPlasmaMutationMAF_from_BAMPrepareLibrary
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArrayDEoptimRfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangrobustbaseRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
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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 |