Files in TVTB

TVTB: The VCF Tool Box

README.md

NAMESPACE

DESCRIPTION

build/vignette.rds

build/partial.rdb

R/addPhenoLevelFrequencies-methods.R R/vepInPhenoLevel-methods.R R/TVTBparam-class.R R/addFrequencies-methods.R R/show-methods.R R/AllGenerics.R R/utils.R R/readVcf-methods.R R/countGenos-methods.R R/pairsInfo.R R/dropInfo.R R/plotInfo.R R/Genotypes-class.R R/addOverallFrequencies-methods.R R/AllClasses.R R/autodetectGenotypes.R R/tSVE.R R/addCountGenos-methods.R R/variantsInSamples-methods.R R/VcfFilterRules-class.R vignettes/VcfFilterRules.Rmd vignettes/tSVE.Rmd vignettes/Introduction.Rmd

vignettes/TVTB.bib

man/countGenos-methods.Rd man/addPhenoLevelFrequencies-methods.Rd man/TVTB-package.Rd man/addFrequencies-methods.Rd man/addCountGenos-methods.Rd man/TVTBParam-class.Rd man/plotInfo-methods.Rd man/variantsInSamples-methods.Rd man/VcfFilterRules-class.Rd man/dropInfo-methods.Rd man/pairsInfo-methods.Rd man/readVcf-methods.Rd man/VcfBasicRules-class.Rd man/Genotypes-class.Rd man/addOverallFrequencies-methods.Rd man/tSVE.Rd man/autodetectGenotypes.Rd man/vepInPhenoLevel-methods.Rd tests/testthat.R tests/testthat/test_vepInPhenoLevel-methods.R tests/testthat/test_addFrequencies-methods.R tests/testthat/test_Genotypes-class.R tests/testthat/test_readVcf-methods.R tests/testthat/test_addOverallFrequencies-methods.R tests/testthat/test_dropInfo.R tests/testthat/test_VcfFilterRules-class.R tests/testthat/test_TVTBparam-class.R tests/testthat/test_plotInfo-methods.R tests/testthat/test_addCountGenos-methods.R tests/testthat/test_variantsInSamples-methods.R tests/testthat/test_autodetectGenotypes-methods.R tests/testthat/test_pairsInfo-methods.R tests/testthat/test_countGenos-methods.R tests/testthat/test_addPhenoLevelFrequencies-methods.R

inst/NEWS.Rd

inst/doc/VcfFilterRules.Rmd

inst/doc/VcfFilterRules.html

inst/doc/VcfFilterRules.R inst/doc/tSVE.Rmd

inst/doc/tSVE.html

inst/doc/Introduction.R inst/doc/Introduction.Rmd inst/doc/tSVE.R

inst/doc/Introduction.html

inst/extdata/ADH1B.bed

inst/extdata/moderate.vcf

inst/extdata/integrated_samples.txt

inst/extdata/SLC24A5.bed

inst/extdata/chr4.phase3_integrated.vcf_summary.html

inst/extdata/moderate.vcf.gz

inst/extdata/moderate.vcf.gz.tbi

inst/extdata/chr15.phase3_integrated.vcf.gz

inst/extdata/chr15.phase3_integrated.vcf.gz.tbi

inst/extdata/chr4.phase3_integrated.vcf.gz.tbi

inst/extdata/chr4.phase3_integrated.vcf.gz

inst/extdata/moderate_pheno.txt

inst/misc/1kgenomes_SLC24A5_VEP.sh

inst/misc/1kgenomes_ADH1B_VEP.sh

inst/misc/motivations_rules.rds

inst/sandbox/tabulateVep-methods.Rd

inst/sandbox/densityVep-methods.Rd

inst/sandbox/SKAT.R inst/sandbox/test_densityVep-methods.R inst/sandbox/tabulateVep-methods.R inst/sandbox/densityVep-methods.R inst/sandbox/test_tabulateVep-methods.R

inst/badexamples/noCSQ.vcf.gz

inst/badexamples/chr3.dummy2.vcf.gz

inst/badexamples/pheno_NoOverlap.txt

inst/badexamples/pheno_PartialOverlap.txt

inst/badexamples/noCSQ.vcf.gz.tbi

inst/badexamples/pheno_OnlyColnames.txt

inst/badexamples/chr3.dummy1.vcf.gz

inst/badexamples/pheno_OnlyRownames.txt

inst/shinyApp/ensembldbFunctions.R inst/shinyApp/serverRoutines.R inst/shinyApp/fileParseFunctions.R inst/shinyApp/ui.R inst/shinyApp/regions2vcf.R inst/shinyApp/server.R inst/shinyApp/grangesParseFunctions.R inst/shinyApp/global.R

inst/shinyApp/doc/EnsDbFilter.Rd

inst/shinyApp/doc/chr2file.Rd

inst/shinyApp/doc/getEdb.Rd

inst/shinyApp/www/bootstrap.css

inst/shinyApp/rds/parallel.rds

TVTB documentation built on Nov. 8, 2020, 6:09 p.m.