TVTB: TVTB: The VCF Tool Box
Version 1.2.0

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]
Bioconductor views Alignment Coverage DNASeq DataImport DataRepresentation GUI GeneticVariability Genetics GenomicVariation MultipleComparison SequenceMatching Sequencing Software VariantAnnotation Visualization WholeGenome
Date of publicationNone
MaintainerKevin Rue-Albrecht <kevinrue67@gmail.com>
LicenseArtistic-2.0
Version1.2.0
URL https://github.com/kevinrue/TVTB
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("TVTB")

Getting started

Package overview
README.md
Introduction to TVTB
The Shiny Variant Explorer
VCF filter rules

Popular man pages

addCountGenos-methods: Add count of genotypes to INFO field
countGenos-methods: Count occurences of genotypes
Genotypes-class: Genotypes class objects
pairsInfo-methods: Plot an INFO metric on a genomic axis.
readVcf-methods: Read VCF files
tSVE: The Shiny Variant Explorer (tSVE) web-application
TVTB-package: TVTB: The VCF Tool Box
See all...

All man pages Function index File listing

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
autodetectGenotypes: Define genotypes in the TVTBparam metadata slot
countGenos-methods: Count occurences of genotypes
dropInfo-methods: Remove INFO keys from VCF objects
Genotypes-class: Genotypes class objects
pairsInfo-methods: Plot an INFO metric on a genomic axis.
plotInfo-methods: Plot an INFO metric on a genomic axis.
readVcf-methods: Read VCF files
tSVE: The Shiny Variant Explorer (tSVE) web-application
TVTB-package: TVTB: The VCF Tool Box
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

Functions

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/Genotypes-class.R
R/TVTBparam-class.R
R/VcfFilterRules-class.R
R/addCountGenos-methods.R
R/addFrequencies-methods.R
R/addOverallFrequencies-methods.R
R/addPhenoLevelFrequencies-methods.R
R/autodetectGenotypes.R
R/countGenos-methods.R
R/dropInfo.R
R/pairsInfo.R
R/plotInfo.R
R/readVcf-methods.R
R/show-methods.R
R/tSVE.R
R/utils.R
R/variantsInSamples-methods.R
R/vepInPhenoLevel-methods.R
README.md
build
build/partial.rdb
build/vignette.rds
inst
inst/NEWS.Rd
inst/badexamples
inst/badexamples/chr3.dummy1.vcf.gz
inst/badexamples/chr3.dummy2.vcf.gz
inst/badexamples/noCSQ.vcf.gz
inst/badexamples/noCSQ.vcf.gz.tbi
inst/badexamples/pheno_NoOverlap.txt
inst/badexamples/pheno_OnlyColnames.txt
inst/badexamples/pheno_OnlyRownames.txt
inst/badexamples/pheno_PartialOverlap.txt
inst/doc
inst/doc/Introduction.R
inst/doc/Introduction.Rmd
inst/doc/Introduction.html
inst/doc/VcfFilterRules.R
inst/doc/VcfFilterRules.Rmd
inst/doc/VcfFilterRules.html
inst/doc/tSVE.R
inst/doc/tSVE.Rmd
inst/doc/tSVE.html
inst/extdata
inst/extdata/ADH1B.bed
inst/extdata/SLC24A5.bed
inst/extdata/chr15.phase3_integrated.vcf.gz
inst/extdata/chr15.phase3_integrated.vcf.gz.tbi
inst/extdata/chr4.phase3_integrated.vcf.gz
inst/extdata/chr4.phase3_integrated.vcf.gz.tbi
inst/extdata/chr4.phase3_integrated.vcf_summary.html
inst/extdata/integrated_samples.txt
inst/extdata/moderate.vcf
inst/extdata/moderate.vcf.gz
inst/extdata/moderate.vcf.gz.tbi
inst/extdata/moderate_pheno.txt
inst/misc
inst/misc/1kgenomes_ADH1B_VEP.sh
inst/misc/1kgenomes_SLC24A5_VEP.sh
inst/misc/motivations_rules.rds
inst/sandbox
inst/sandbox/SKAT.R
inst/sandbox/densityVep-methods.R
inst/sandbox/densityVep-methods.Rd
inst/sandbox/tabulateVep-methods.R
inst/sandbox/tabulateVep-methods.Rd
inst/sandbox/test_densityVep-methods.R
inst/sandbox/test_tabulateVep-methods.R
inst/shinyApp
inst/shinyApp/doc
inst/shinyApp/doc/EnsDbFilter.Rd
inst/shinyApp/doc/chr2file.Rd
inst/shinyApp/doc/getEdb.Rd
inst/shinyApp/ensembldbFunctions.R
inst/shinyApp/fileParseFunctions.R
inst/shinyApp/global.R
inst/shinyApp/grangesParseFunctions.R
inst/shinyApp/rds
inst/shinyApp/rds/parallel.rds
inst/shinyApp/regions2vcf.R
inst/shinyApp/server.R
inst/shinyApp/serverRoutines.R
inst/shinyApp/ui.R
inst/shinyApp/www
inst/shinyApp/www/bootstrap.css
man
man/Genotypes-class.Rd
man/TVTB-package.Rd
man/TVTBParam-class.Rd
man/VcfBasicRules-class.Rd
man/VcfFilterRules-class.Rd
man/addCountGenos-methods.Rd
man/addFrequencies-methods.Rd
man/addOverallFrequencies-methods.Rd
man/addPhenoLevelFrequencies-methods.Rd
man/autodetectGenotypes.Rd
man/countGenos-methods.Rd
man/dropInfo-methods.Rd
man/pairsInfo-methods.Rd
man/plotInfo-methods.Rd
man/readVcf-methods.Rd
man/tSVE.Rd
man/variantsInSamples-methods.Rd
man/vepInPhenoLevel-methods.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_Genotypes-class.R
tests/testthat/test_TVTBparam-class.R
tests/testthat/test_VcfFilterRules-class.R
tests/testthat/test_addCountGenos-methods.R
tests/testthat/test_addFrequencies-methods.R
tests/testthat/test_addOverallFrequencies-methods.R
tests/testthat/test_addPhenoLevelFrequencies-methods.R
tests/testthat/test_autodetectGenotypes-methods.R
tests/testthat/test_countGenos-methods.R
tests/testthat/test_dropInfo.R
tests/testthat/test_pairsInfo-methods.R
tests/testthat/test_plotInfo-methods.R
tests/testthat/test_readVcf-methods.R
tests/testthat/test_variantsInSamples-methods.R
tests/testthat/test_vepInPhenoLevel-methods.R
vignettes
vignettes/Introduction.Rmd
vignettes/TVTB.bib
vignettes/VcfFilterRules.Rmd
vignettes/tSVE.Rmd
TVTB documentation built on May 20, 2017, 10:01 p.m.

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