# TVTB: The VCF Tool Box

## Documentation for package ‘TVTB’ version 1.35.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E G H I M P R S T V misc

TVTB-package | TVTB: The VCF Tool Box

## -- A --

aaf | TVTBparam class objects
aaf-method | TVTBparam class objects
aaf<- | TVTBparam class objects
aaf<--method | TVTBparam class objects
addCountGenos | Add count of genotypes to INFO field
addCountGenos-method | Add count of genotypes to INFO field
addCountGenos-methods | Add count of genotypes to INFO field
addFrequencies | Group-level genotypes counts and allele frequencies
addFrequencies-method | Group-level genotypes counts and allele frequencies
addFrequencies-methods | Group-level genotypes counts and allele frequencies
addOverallFrequencies | Overall genotypes counts and allele frequencies
addOverallFrequencies-method | Overall genotypes counts and allele frequencies
addOverallFrequencies-methods | Overall genotypes counts and allele frequencies
addPhenoLevelFrequencies | Genotypes and allele frequencies for a given phenotype level
addPhenoLevelFrequencies-method | Genotypes and allele frequencies for a given phenotype level
addPhenoLevelFrequencies-methods | Genotypes and allele frequencies for a given phenotype level
alt-method | Genotypes class objects
alt-method | TVTBparam class objects
alt<--method | Genotypes class objects
alt<--method | TVTBparam class objects
append-method | VCF filters class objects sub-types
append-method | VcfFilterRules class objects
autodetectGenotypes | Define genotypes in the TVTBparam metadata slot
autodetectGenotypes-method | Define genotypes in the TVTBparam metadata slot
autodetectGenotypes-methods | Define genotypes in the TVTBparam metadata slot

## -- B --

bp | TVTBparam class objects
bp-method | TVTBparam class objects
bp<- | TVTBparam class objects
bp<--method | TVTBparam class objects

## -- C --

c-method | VCF filters class objects sub-types
c-method | VcfFilterRules class objects
carrier | Genotypes class objects
carrier-method | Genotypes class objects
carrier-method | TVTBparam class objects
class:Genotypes | Genotypes class objects
class:TVTBparam | TVTBparam class objects
class:VcfFilterRules | VcfFilterRules class objects
class:VcfFixedRules | VCF filters class objects sub-types
class:VcfInfoRules | VCF filters class objects sub-types
class:VcfVepRules | VCF filters class objects sub-types
countGenos | Count occurences of genotypes
countGenos-method | Count occurences of genotypes
countGenos-methods | Count occurences of genotypes

## -- D --

dropInfo | Remove INFO keys from VCF objects
dropInfo-method | Remove INFO keys from VCF objects
dropInfo-methods | Remove INFO keys from VCF objects

## -- E --

eval-method | VCF filters class objects sub-types
eval-method | VcfFilterRules class objects

## -- G --

genos | Genotypes class objects
genos-method | Genotypes class objects
genos-method | TVTBparam class objects
genos<- | TVTBparam class objects
genos<--method | TVTBparam class objects
Genotypes | Genotypes class objects
Genotypes-class | Genotypes class objects
Genotypes-methods | Genotypes class objects

## -- H --

het | Genotypes class objects
het-method | Genotypes class objects
het-method | TVTBparam class objects
het<- | Genotypes class objects
het<--method | Genotypes class objects
het<--method | TVTBparam class objects

## -- I --

initialize-method | Genotypes class objects
initialize-method | TVTBparam class objects
initialize-method | VCF filters class objects sub-types
initialize-method | VcfFilterRules class objects

## -- M --

maf | TVTBparam class objects
maf-method | TVTBparam class objects
maf<- | TVTBparam class objects
maf<--method | TVTBparam class objects

## -- P --

pairsInfo | Plot an INFO metric on a genomic axis.
pairsInfo-method | Plot an INFO metric on a genomic axis.
pairsInfo-methods | Plot an INFO metric on a genomic axis.
parseCSQToGRanges | Parse the CSQ column of a VCF object into a GRanges object
parseCSQToGRanges-method | Parse the CSQ column of a VCF object into a GRanges object
plotInfo | Plot an INFO metric on a genomic axis.
plotInfo-method | Plot an INFO metric on a genomic axis.
plotInfo-methods | Plot an INFO metric on a genomic axis.

## -- R --

ranges | TVTBparam class objects
ranges-method | TVTBparam class objects
ranges<- | TVTBparam class objects
ranges<--method | TVTBparam class objects
readVcf-method | Read VCF files
ref-method | Genotypes class objects
ref-method | TVTBparam class objects
ref<--method | Genotypes class objects
ref<--method | TVTBparam class objects

## -- S --

suffix | Genotypes class objects
suffix-method | Genotypes class objects
suffix-method | TVTBparam class objects
svp | TVTBparam class objects
svp-method | TVTBparam class objects
svp<- | TVTBparam class objects
svp<--method | TVTBparam class objects

## -- T --

tSVE | The Shiny Variant Explorer (tSVE) web-application
TVTBparam | TVTBparam class objects
TVTBparam-class | TVTBparam class objects
TVTBparam-methods | TVTBparam class objects
type-method | VCF filters class objects sub-types
type-method | VcfFilterRules class objects

## -- V --

variantsInSamples | Identify variants observed in samples
variantsInSamples-method | Identify variants observed in samples
variantsInSamples-methods | Identify variants observed in samples
VcfFilterRules | VcfFilterRules class objects
VcfFilterRules-class | VcfFilterRules class objects
VcfFixedRules | VCF filters class objects sub-types
VcfFixedRules-class | VCF filters class objects sub-types
VcfInfoRules | VCF filters class objects sub-types
VcfInfoRules-class | VCF filters class objects sub-types
VcfVepRules | VCF filters class objects sub-types
VcfVepRules-class | VCF filters class objects sub-types
vep | TVTBparam class objects
vep-method | TVTBparam class objects
vep-method | VCF filters class objects sub-types
vep-method | VcfFilterRules class objects
vep<- | TVTBparam class objects
vep<--method | TVTBparam class objects
vep<--method | VCF filters class objects sub-types
vep<--method | VcfFilterRules class objects
vepInPhenoLevel | VEP predictions of variants observed in samples
vepInPhenoLevel-method | VEP predictions of variants observed in samples
vepInPhenoLevel-methods | VEP predictions of variants observed in samples

## -- misc --

[-method | VCF filters class objects sub-types
[-method | VcfFilterRules class objects
[<--method | VCF filters class objects sub-types
[<--method | VcfFilterRules class objects
[[-method | VCF filters class objects sub-types
[[-method | VcfFilterRules class objects
[[<--method | VCF filters class objects sub-types
[[<--method | VcfFilterRules class objects