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).

AuthorKevin Rue-Albrecht [aut, cre]
Date of publicationNone
MaintainerKevin Rue-Albrecht <kevinrue67@gmail.com>
LicenseArtistic-2.0
Version1.0.2
https://github.com/kevinrue/TVTB

View on Bioconductor

Functions

aaf Man page
aaf<- Man page
aaf<-,TVTBparam,character-method Man page
aaf,TVTBparam-method Man page
addCountGenos Man page
addCountGenos,ExpandedVCF-method Man page
addCountGenos-methods Man page
addFrequencies Man page
addFrequencies,ExpandedVCF,character-method Man page
addFrequencies,ExpandedVCF,list-method Man page
addFrequencies,ExpandedVCF,missing-method Man page
addFrequencies-methods Man page
addOverallFrequencies Man page
addOverallFrequencies,ExpandedVCF-method Man page
addOverallFrequencies-methods Man page
addPhenoLevelFrequencies Man page
addPhenoLevelFrequencies,ExpandedVCF-method Man page
addPhenoLevelFrequencies-methods Man page
alt<-,Genotypes,character-method Man page
alt,Genotypes-method Man page
alt<-,TVTBparam,character-method Man page
alt<-,TVTBparam,list-method Man page
alt,TVTBparam-method Man page
append,VcfFilterRules,FilterRules-method Man page
append,VcfFixedRules,FilterRules-method Man page
append,VcfInfoRules,FilterRules-method Man page
append,VcfVepRules,FilterRules-method Man page
bp Man page
bp<- Man page
bp<-,TVTBparam,BiocParallelParam-method Man page
bp,TVTBparam-method Man page
carrier Man page
carrier,Genotypes-method Man page
carrier,TVTBparam-method Man page
class:Genotypes Man page
class:TVTBparam Man page
class:VcfFilterRules Man page
class:VcfFixedRules Man page
class:VcfInfoRules Man page
class:VcfVepRules Man page
countGenos Man page
countGenos,ExpandedVCF-method Man page
countGenos-methods Man page
c,VcfFilterRules-method Man page
c,VcfFixedRules-method Man page
c,VcfInfoRules-method Man page
c,VcfVepRules-method Man page
dropInfo Man page
dropInfo-methods Man page
dropInfo,VCF-method Man page
eval,VcfFilterRules,VCF-method Man page
eval,VcfFixedRules,VCF-method Man page
eval,VcfInfoRules,VCF-method Man page
eval,VcfVepRules,VCF-method Man page
genos Man page
genos<- Man page
genos,Genotypes-method Man page
genos<-,TVTBparam,Genotypes-method Man page
genos,TVTBparam-method Man page
Genotypes Man page
Genotypes,character,character,character-method Man page
Genotypes-class Man page
Genotypes-methods Man page
het Man page
het<- Man page
het<-,Genotypes,character-method Man page
het,Genotypes-method Man page
het<-,TVTBparam,character-method Man page
het<-,TVTBparam,list-method Man page
het,TVTBparam-method Man page
initialize,Genotypes-method Man page
initialize,TVTBparam-method Man page
initialize,VcfFilterRules-method Man page
initialize,VcfFixedRules-method Man page
initialize,VcfInfoRules-method Man page
initialize,VcfVepRules-method Man page
maf Man page
maf<- Man page
maf<-,TVTBparam,character-method Man page
maf,TVTBparam-method Man page
ranges Man page
ranges<- Man page
ranges<-,TVTBparam,GRangesList-method Man page
ranges,TVTBparam-method Man page
readVcf,character,TVTBparam-method Man page
readVcf,TabixFile,TVTBparam-method Man page
ref<-,Genotypes,character-method Man page
ref,Genotypes-method Man page
ref<-,TVTBparam,character-method Man page
ref<-,TVTBparam,list-method Man page
ref,TVTBparam-method Man page
suffix Man page
suffix,Genotypes-method Man page
suffix,TVTBparam-method Man page
svp Man page
svp<- Man page
svp,TVTBparam-method Man page
svp<-,TVTBparam,ScanVcfParam-method Man page
tSVE Man page
TVTB-package Man page
TVTBparam Man page
TVTBparam-class Man page
TVTBparam,Genotypes-method Man page
TVTBparam-methods Man page
type,FilterRules-method Man page
type,VcfFilterRules-method Man page
type,VcfFixedRules-method Man page
type,VcfInfoRules-method Man page
type,VcfVepRules-method Man page
variantsInSamples Man page
variantsInSamples,ExpandedVCF-method Man page
variantsInSamples-methods Man page
VcfFilterRules Man page
[,VcfFilterRules,ANY,ANY,ANY-method Man page
[,VcfFilterRules,ANY,ANY,logical-method Man page
[[<-,VcfFilterRules,ANY,ANY-method Man page
[[,VcfFilterRules,ANY,ANY-method Man page
[,VcfFilterRules,ANY,ANY,missing-method Man page
VcfFilterRules,ANY-method Man page
VcfFilterRules-class Man page
[<-,VcfFilterRules,numeric,missing,VcfFilterRules-method Man page
[<-,VcfFilterRules,numeric,missing,VcfFixedRules-method Man page
[<-,VcfFilterRules,numeric,missing,VcfInfoRules-method Man page
[<-,VcfFilterRules,numeric,missing,VcfVepRules-method Man page
VcfFixedRules Man page
VcfFixedRules Man page
[,VcfFixedRules,ANY,ANY-method Man page
[[<-,VcfFixedRules,ANY,ANY-method Man page
[[,VcfFixedRules,ANY,ANY-method Man page
VcfFixedRules-class Man page
[<-,VcfFixedRules,numeric,missing,VcfFixedRules-method Man page
VcfInfoRules Man page
VcfInfoRules Man page
[,VcfInfoRules,ANY,ANY-method Man page
[[<-,VcfInfoRules,ANY,ANY-method Man page
[[,VcfInfoRules,ANY,ANY-method Man page
VcfInfoRules-class Man page
[<-,VcfInfoRules,numeric,missing,VcfInfoRules-method Man page
VcfVepRules Man page
VcfVepRules Man page
[,VcfVepRules,ANY,ANY-method Man page
[[<-,VcfVepRules,ANY,ANY-method Man page
[[,VcfVepRules,ANY,ANY-method Man page
VcfVepRules-class Man page
[<-,VcfVepRules,numeric,missing,VcfVepRules-method Man page
vep Man page
vep<- Man page
vep,FilterRules-method Man page
vepInPhenoLevel Man page
vepInPhenoLevel,ExpandedVCF-method Man page
vepInPhenoLevel-methods Man page
vep<-,TVTBparam,character-method Man page
vep,TVTBparam-method Man page
vep<-,VcfFilterRules,character-method Man page
vep,VcfFilterRules-method Man page
vep,VcfFixedRules-method Man page
vep,VcfInfoRules-method Man page
vep<-,VcfVepRules,character-method Man page
vep,VcfVepRules-method Man page

Files

TVTB/DESCRIPTION
TVTB/NAMESPACE
TVTB/R
TVTB/R/AllClasses.R TVTB/R/AllGenerics.R TVTB/R/Genotypes-class.R TVTB/R/TVTBparam-class.R TVTB/R/VcfFilterRules-class.R TVTB/R/addCountGenos-methods.R TVTB/R/addFrequencies-methods.R TVTB/R/addOverallFrequencies-methods.R TVTB/R/addPhenoLevelFrequencies-methods.R TVTB/R/countGenos-methods.R TVTB/R/dropInfo.R TVTB/R/readVcf-methods.R TVTB/R/show-methods.R TVTB/R/tSVE.R TVTB/R/variantsInSamples-methods.R TVTB/R/vepInPhenoLevel-methods.R
TVTB/README.md
TVTB/build
TVTB/build/partial.rdb
TVTB/build/vignette.rds
TVTB/inst
TVTB/inst/NEWS.Rd
TVTB/inst/badexamples
TVTB/inst/badexamples/chr3.dummy1.vcf.gz
TVTB/inst/badexamples/chr3.dummy2.vcf.gz
TVTB/inst/badexamples/noCSQ.vcf.gz
TVTB/inst/badexamples/noCSQ.vcf.gz.tbi
TVTB/inst/badexamples/pheno_NoOverlap.txt
TVTB/inst/badexamples/pheno_PartialOverlap.txt
TVTB/inst/doc
TVTB/inst/doc/Introduction.R
TVTB/inst/doc/Introduction.Rmd
TVTB/inst/doc/Introduction.html
TVTB/inst/doc/VcfFilterRules.R
TVTB/inst/doc/VcfFilterRules.Rmd
TVTB/inst/doc/VcfFilterRules.html
TVTB/inst/doc/tSVE.R
TVTB/inst/doc/tSVE.Rmd
TVTB/inst/doc/tSVE.html
TVTB/inst/extdata
TVTB/inst/extdata/SLC24A5.bed
TVTB/inst/extdata/chr15.phase3_integrated.vcf.gz
TVTB/inst/extdata/chr15.phase3_integrated.vcf.gz.tbi
TVTB/inst/extdata/integrated_samples.txt
TVTB/inst/extdata/moderate.vcf
TVTB/inst/extdata/moderate.vcf.gz
TVTB/inst/extdata/moderate.vcf.gz.tbi
TVTB/inst/extdata/moderate_pheno.txt
TVTB/inst/misc
TVTB/inst/misc/1kgenomes_SLC24A5_VEP.sh
TVTB/inst/misc/quickFilterTest.R
TVTB/inst/misc/subset_moderate_samples.R
TVTB/inst/misc/tSVE.xmind
TVTB/inst/sandbox
TVTB/inst/sandbox/densityVep-methods.R
TVTB/inst/sandbox/densityVep-methods.Rd
TVTB/inst/sandbox/tabulateVep-methods.R
TVTB/inst/sandbox/tabulateVep-methods.Rd
TVTB/inst/sandbox/test_densityVep-methods.R
TVTB/inst/sandbox/test_tabulateVep-methods.R
TVTB/inst/shinyApp
TVTB/inst/shinyApp/doc
TVTB/inst/shinyApp/doc/EnsDbFilter.Rd
TVTB/inst/shinyApp/doc/chr2file.Rd
TVTB/inst/shinyApp/doc/getEdb.Rd
TVTB/inst/shinyApp/ensembldbFunctions.R
TVTB/inst/shinyApp/fileParseFunctions.R
TVTB/inst/shinyApp/global.R
TVTB/inst/shinyApp/grangesParseFunctions.R
TVTB/inst/shinyApp/regions2vcf.R
TVTB/inst/shinyApp/server.R
TVTB/inst/shinyApp/serverRoutines.R
TVTB/inst/shinyApp/ui.R
TVTB/inst/shinyApp/www
TVTB/inst/shinyApp/www/bootstrap.css
TVTB/man
TVTB/man/Genotypes-class.Rd TVTB/man/TVTB-package.Rd TVTB/man/TVTBParam-class.Rd TVTB/man/VcfBasicRules-class.Rd TVTB/man/VcfFilterRules-class.Rd TVTB/man/addCountGenos-methods.Rd TVTB/man/addFrequencies-methods.Rd TVTB/man/addOverallFrequencies-methods.Rd TVTB/man/addPhenoLevelFrequencies-methods.Rd TVTB/man/countGenos-methods.Rd TVTB/man/dropInfo-methods.Rd TVTB/man/readVcf-methods.Rd TVTB/man/tSVE.Rd TVTB/man/variantsInSamples-methods.Rd TVTB/man/vepInPhenoLevel-methods.Rd
TVTB/tests
TVTB/tests/testthat
TVTB/tests/testthat.R
TVTB/tests/testthat/test_Genotypes-class.R
TVTB/tests/testthat/test_TVTBparam-class.R
TVTB/tests/testthat/test_VcfFilterRules-class.R
TVTB/tests/testthat/test_addCountGenos-methods.R
TVTB/tests/testthat/test_addFrequencies-methods.R
TVTB/tests/testthat/test_addOverallFrequencies-methods.R
TVTB/tests/testthat/test_addPhenoLevelFrequencies-methods.R
TVTB/tests/testthat/test_countGenos-methods.R
TVTB/tests/testthat/test_dropInfo.R
TVTB/tests/testthat/test_readVcf-methods.R
TVTB/tests/testthat/test_variantsInSamples-methods.R
TVTB/tests/testthat/test_vepInPhenoLevel-methods.R
TVTB/vignettes
TVTB/vignettes/Introduction.Rmd
TVTB/vignettes/TVTB.bib
TVTB/vignettes/VcfFilterRules.Rmd
TVTB/vignettes/tSVE.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.