Package: TVTB 1.31.1

Kevin Rue-Albrecht

TVTB: TVTB: The VCF Tool Box

The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

Authors:Kevin Rue-Albrecht [aut, cre]

TVTB_1.31.1.tar.gz
TVTB_1.31.1.zip(r-4.5)TVTB_1.31.1.zip(r-4.4)TVTB_1.31.1.zip(r-4.3)
TVTB_1.31.1.tgz(r-4.4-any)TVTB_1.31.1.tgz(r-4.3-any)
TVTB_1.31.1.tar.gz(r-4.5-noble)TVTB_1.31.1.tar.gz(r-4.4-noble)
TVTB_1.31.1.tgz(r-4.4-emscripten)TVTB_1.31.1.tgz(r-4.3-emscripten)
TVTB.pdf |TVTB.html✨
TVTB/json (API)
NEWS

# Install 'TVTB' in R:
install.packages('TVTB', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/kevinrue/tvtb/issues

On BioConductor:TVTB-1.31.0(bioc 3.20)TVTB-1.30.0(bioc 3.19)

bioconductor-package

61 exports 0.82 score 163 dependencies

Last updated 6 days agofrom:1a281a092b

Exports:aafaaf<-activeactive<-addCountGenosaddFrequenciesaddOverallFrequenciesaddPhenoLevelFrequenciesaltalt<-appendautodetectGenotypesbpbp<-carriercolDatacolData<-countGenosdropInfoevalevalSeparatelyfixedgenogenosgenos<-Genotypesheaderheader<-hethet<-infoinfo<-mafmaf<-mcolsmetadatametadata<-pairsInfoparseCSQToGRangesplotInforangesranges<-readVcfrefref<-ScanVcfParamsubsetByFiltersuffixsvpsvp<-tSVETVTBparamtypevariantsInSamplesVcfFilterRulesVcfFixedRulesVcfInfoRulesVcfVepRulesvepvep<-vepInPhenoLevel

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobbroombroom.helpersBSgenomebslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggplot2ggstatsgluegridExtragtableGvizhavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglabelledlambda.rlatticelatticeExtralazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpatchworkpillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2XVectoryamlzlibbioc

Introduction to TVTB

Kévin Rue-Albrecht

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Jul 05 2024.

Last update: 2018-07-20
Started: 2016-10-13

The Shiny Variant Explorer

Kévin Rue-Albrecht

Rendered fromtSVE.Rmdusingknitr::rmarkdownon Jul 05 2024.

Last update: 2020-04-11
Started: 2016-10-13

VCF filter rules

Kévin Rue-Albrecht

Rendered fromVcfFilterRules.Rmdusingknitr::rmarkdownon Jul 05 2024.

Last update: 2024-07-04
Started: 2016-10-13

Readme and manuals

Help Manual

Help pageTopics
TVTB: The VCF Tool BoxTVTB-package
Add count of genotypes to INFO fieldaddCountGenos addCountGenos,ExpandedVCF-method addCountGenos-methods
Group-level genotypes counts and allele frequenciesaddFrequencies addFrequencies,ExpandedVCF,character-method addFrequencies,ExpandedVCF,list-method addFrequencies,ExpandedVCF,missing-method addFrequencies-methods
Overall genotypes counts and allele frequenciesaddOverallFrequencies addOverallFrequencies,ExpandedVCF-method addOverallFrequencies-methods
Genotypes and allele frequencies for a given phenotype leveladdPhenoLevelFrequencies addPhenoLevelFrequencies,ExpandedVCF-method addPhenoLevelFrequencies-methods
Define genotypes in the TVTBparam metadata slotautodetectGenotypes autodetectGenotypes,VCF-method autodetectGenotypes-methods
Count occurences of genotypescountGenos countGenos,ExpandedVCF-method countGenos-methods
Remove INFO keys from VCF objectsdropInfo dropInfo,VCF-method dropInfo-methods
Genotypes class objectsalt,Genotypes-method alt<-,Genotypes,character-method carrier carrier,Genotypes-method class:Genotypes genos genos,Genotypes-method Genotypes Genotypes-class Genotypes-methods het het,Genotypes-method het<- het<-,Genotypes,character-method initialize,Genotypes-method ref,Genotypes-method ref<-,Genotypes,character-method suffix suffix,Genotypes-method
Plot an INFO metric on a genomic axis.pairsInfo pairsInfo,VCF-method pairsInfo-methods
Parse the CSQ column of a VCF object into a GRanges objectparseCSQToGRanges parseCSQToGRanges,VCF-method
Plot an INFO metric on a genomic axis.plotInfo plotInfo,VCF-method plotInfo-methods
Read VCF filesreadVcf,character,TVTBparam-method readVcf,TabixFile,TVTBparam-method
The Shiny Variant Explorer (tSVE) web-applicationtSVE
TVTBparam class objectsaaf aaf,TVTBparam-method aaf<- aaf<-,TVTBparam,character-method alt,TVTBparam-method alt<-,TVTBparam,character-method alt<-,TVTBparam,list-method bp bp,TVTBparam-method bp<- bp<-,TVTBparam,BiocParallelParam-method carrier,TVTBparam-method class:TVTBparam genos,TVTBparam-method genos<- genos<-,TVTBparam,Genotypes-method het,TVTBparam-method het<-,TVTBparam,character-method het<-,TVTBparam,list-method initialize,TVTBparam-method maf maf,TVTBparam-method maf<- maf<-,TVTBparam,character-method ranges ranges,TVTBparam-method ranges<- ranges<-,TVTBparam,GRangesList-method ref,TVTBparam-method ref<-,TVTBparam,character-method ref<-,TVTBparam,list-method suffix,TVTBparam-method svp svp,TVTBparam-method svp<- svp<-,TVTBparam,ScanVcfParam-method TVTBparam TVTBparam-class TVTBparam-methods vep vep,TVTBparam-method vep<- vep<-,TVTBparam,character-method
Identify variants observed in samplesvariantsInSamples variantsInSamples,ExpandedVCF-method variantsInSamples-methods
VCF filters class objects sub-typesappend,VcfFixedRules,FilterRules-method append,VcfInfoRules,FilterRules-method append,VcfVepRules,FilterRules-method c,VcfFixedRules-method c,VcfInfoRules-method c,VcfVepRules-method class:VcfFixedRules class:VcfInfoRules class:VcfVepRules eval,VcfFixedRules,VCF-method eval,VcfInfoRules,VCF-method eval,VcfVepRules,VCF-method initialize,VcfFixedRules-method initialize,VcfInfoRules-method initialize,VcfVepRules-method type,FilterRules-method type,VcfFixedRules-method type,VcfInfoRules-method type,VcfVepRules-method VcfFixedRules VcfFixedRules-class VcfInfoRules VcfInfoRules-class VcfVepRules VcfVepRules-class vep,FilterRules-method vep,VcfFixedRules-method vep,VcfInfoRules-method vep,VcfVepRules-method vep<-,VcfVepRules,character-method [,VcfFixedRules,ANY,ANY-method [,VcfInfoRules,ANY,ANY-method [,VcfVepRules,ANY,ANY-method [<-,VcfFixedRules,numeric,missing,VcfFixedRules-method [<-,VcfInfoRules,numeric,missing,VcfInfoRules-method [<-,VcfVepRules,numeric,missing,VcfVepRules-method [[,VcfFixedRules,ANY,ANY-method [[,VcfInfoRules,ANY,ANY-method [[,VcfVepRules,ANY,ANY-method [[<-,VcfFixedRules,ANY,ANY-method [[<-,VcfInfoRules,ANY,ANY-method [[<-,VcfVepRules,ANY,ANY-method
VcfFilterRules class objectsappend,VcfFilterRules,FilterRules-method c,VcfFilterRules-method class:VcfFilterRules eval,VcfFilterRules,VCF-method initialize,VcfFilterRules-method type,VcfFilterRules-method VcfFilterRules VcfFilterRules-class vep,VcfFilterRules-method vep<-,VcfFilterRules,character-method [,VcfFilterRules,ANY,ANY,ANY-method [,VcfFilterRules,ANY,ANY,logical-method [,VcfFilterRules,ANY,ANY,missing-method [<-,VcfFilterRules,numeric,missing,VcfFilterRules-method [<-,VcfFilterRules,numeric,missing,VcfFixedRules-method [<-,VcfFilterRules,numeric,missing,VcfInfoRules-method [<-,VcfFilterRules,numeric,missing,VcfVepRules-method [[,VcfFilterRules,ANY,ANY-method [[<-,VcfFilterRules,ANY,ANY-method
VEP predictions of variants observed in samplesvepInPhenoLevel vepInPhenoLevel,ExpandedVCF-method vepInPhenoLevel-methods