Package: TVTB 1.39.0

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_1.39.0.tar.gz
TVTB_1.39.0.zip(r-4.7)TVTB_1.39.0.zip(r-4.6)TVTB_1.39.0.zip(r-4.5)
TVTB_1.39.0.tgz(r-4.6-any)TVTB_1.39.0.tgz(r-4.5-any)
TVTB_1.39.0.tar.gz(r-4.7-any)TVTB_1.39.0.tar.gz(r-4.6-any)
TVTB_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TVTB/json (API)

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

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

On BioConductor:TVTB-1.39.0(bioc 3.24)TVTB-1.38.0(bioc 3.23)

softwaregeneticsgeneticvariabilitygenomicvariationdatarepresentationguidnaseqwholegenomevisualizationmultiplecomparisondataimportvariantannotationsequencingcoveragealignmentsequencematching

5.98 score 2 stars 16 scripts 61 exports 151 dependencies

Last updated from:c77deb7c91. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR302
linux-devel-x86_64WARNING591
source / vignettesOK402
linux-release-x86_64WARNING572
macos-release-arm64WARNING667
macos-oldrel-arm64WARNING262
windows-develWARNING474
windows-releaseWARNING435
windows-oldrelWARNING465
wasm-releaseOK268

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

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggplot2ggstatsgluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpatchworkpillarpkgconfigplyrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml

VCF filter rules
Motivation | Background | Features | Demonstration data | CollapsedVCF and ExpandedVCF | Fields available for the definition of filter rules | Usage of VCF filter rules | Filter rules using a single field | Filter rules using multiple fields | Calculations in filter rules | Functions in filter rules | Pattern matching in filter rules | Using ALT data in the fixed slot of VCF objects | ExpandedVCF objects | CollapsedVCF objects | Combination of multiple types of VCF filter rules | Session info | References
Rendered fromVcfFilterRules.Rmdusingknitr::rmarkdown

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

The Shiny Variant Explorer
Preliminary notes | Pre-requisites | Launching the Shiny Variant Explorer | Overall layout of the web-application | Input panel | Phenotypes | Genomic ranges | BED file | UCSC format | Ensembl-based annotation packages | Variants | Single-VCF mode | Multi-VCF mode | VCF scan parameters | Annotations | Frequencies panel | Overall frequencies | Phenotype-level frequencies | Filters panel | Views panel | Plots panel | Settings panel | Advanced settings | Genotypes | INFO key suffixes | Miscellaneous settings | Parallel settings | Session information | Global configuration | Vignette session | References
Rendered fromtSVE.Rmdusingknitr::rmarkdown

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

Introduction to TVTB
Introduction | Installation | Recurrent settings: TVTBparam | Data import | Genetic variants | List of genomic ranges | Phenotypes | Example | Adding allele frequencies | Adding overall frequencies | Adding frequencies within phenotype level(s) | Filtering variants | Definition of VCF filter rules | Control of VCF filter rules | Evaluation of VCF filter rules | Visualising data | Visualise INFO data by phenotype level on a genomic axis | Pairwise comparison of INFO data between phenotype levels | A taste of future... | Summarising Ensembl VEP predictions | Acknowledgement | Session info | References
Rendered fromIntroduction.Rmdusingknitr::rmarkdown

Last update: 2018-07-20
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