Files in TVTB

TVTB: The VCF Tool Box

README.md 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 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/doc/VcfFilterRules.Rmd inst/doc/VcfFilterRules.R inst/doc/tSVE.Rmd inst/doc/Introduction.R inst/doc/Introduction.Rmd inst/doc/tSVE.R 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/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