TVTB: TVTB: The VCF Tool Box

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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).

Author
Kevin Rue-Albrecht [aut, cre]
Date of publication
None
Maintainer
Kevin Rue-Albrecht <kevinrue67@gmail.com>
License
Artistic-2.0
Version
1.0.2
URLs

View on Bioconductor

Man pages

addCountGenos-methods
Add count of genotypes to INFO field
addFrequencies-methods
Group-level genotypes counts and allele frequencies
addOverallFrequencies-methods
Overall genotypes counts and allele frequencies
addPhenoLevelFrequencies-methods
Genotypes and allele frequencies for a given phenotype level
countGenos-methods
Count occurences of genotypes
dropInfo-methods
Remove INFO keys from VCF objects
Genotypes-class
Genotypes class objects
readVcf-methods
Read VCF files
tSVE
The Shiny Variant Explorer (tSVE) web-application
TVTB-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("TVTB")}
TVTBParam-class
TVTBparam class objects
variantsInSamples-methods
Identify variants observed in samples
VcfBasicRules-class
VCF filters class objects sub-types
VcfFilterRules-class
VcfFilterRules class objects
vepInPhenoLevel-methods
VEP predictions of variants observed in samples

Files in this package

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