API for TVTB
TVTB: The VCF Tool Box

Global functions
.VcfBasicRules	Source code
.addCountGenos	Source code
.addFrequencies	Source code
.addOverallFrequencies	Source code
.addPhenoLevelFrequencies	Source code
.autodetectGenotypes	Source code
.checkInputsPLF	Source code
.checkOverallInfo	Source code
.checkPLFInfo	Source code
.checkParam	Source code
.checkPhenoLevel	Source code
.countGenos	Source code
.dropInfo	Source code
.dropInfoData	Source code
.dropInfoHeader	Source code
.dropVcfFilterRules	Source code
.evalVepFilter	Source code
.findInfoMetricColumns	Source code
.geneRegionTrackFromEnsDb	Source code
.pairsInfo	Source code
.plotInfo	Source code
.readVcf	Source code
.valid.Genotypes	Source code
.valid.TVTBparam	Source code
.valid.VcfBasicRules	Source code
.valid.VcfFilterRules	Source code
.valid.VcfVepRules	Source code
.variantsInSamples	Source code
.vepInPhenoLevel	Source code
Genotypes	Man page Source code
Genotypes-class	Man page
Genotypes-methods	Man page
TVTB-package	Man page
TVTBparam	Man page Source code
TVTBparam-class	Man page
TVTBparam-methods	Man page
VcfFilterRules	Man page Source code
VcfFilterRules,ANY-method	Man page
VcfFilterRules-class	Man page
VcfFixedRules	Man page Man page Source code
VcfFixedRules-class	Man page
VcfInfoRules	Man page Man page Source code
VcfInfoRules-class	Man page
VcfVepRules	Man page Man page Source code
VcfVepRules-class	Man page
[,VcfFilterRules,ANY,ANY,ANY-method	Man page
[,VcfFilterRules,ANY,ANY,logical-method	Man page
[,VcfFilterRules,ANY,ANY,missing-method	Man page
[,VcfFixedRules,ANY,ANY-method	Man page
[,VcfInfoRules,ANY,ANY-method	Man page
[,VcfVepRules,ANY,ANY-method	Man page
[<-,VcfFilterRules,numeric,missing,VcfFilterRules-method	Man page
[<-,VcfFilterRules,numeric,missing,VcfFixedRules-method	Man page
[<-,VcfFilterRules,numeric,missing,VcfInfoRules-method	Man page
[<-,VcfFilterRules,numeric,missing,VcfVepRules-method	Man page
[<-,VcfFixedRules,numeric,missing,VcfFixedRules-method	Man page
[<-,VcfInfoRules,numeric,missing,VcfInfoRules-method	Man page
[<-,VcfVepRules,numeric,missing,VcfVepRules-method	Man page
[[,VcfFilterRules,ANY,ANY-method	Man page
[[,VcfFixedRules,ANY,ANY-method	Man page
[[,VcfInfoRules,ANY,ANY-method	Man page
[[,VcfVepRules,ANY,ANY-method	Man page
[[<-,VcfFilterRules,ANY,ANY-method	Man page
[[<-,VcfFixedRules,ANY,ANY-method	Man page
[[<-,VcfInfoRules,ANY,ANY-method	Man page
[[<-,VcfVepRules,ANY,ANY-method	Man page
aaf	Man page
aaf,TVTBparam-method	Man page
aaf<-	Man page
aaf<-,TVTBparam,character-method	Man page
addCountGenos	Man page
addCountGenos,ExpandedVCF-method	Man page
addCountGenos-methods	Man page
addFrequencies	Man page
addFrequencies,ExpandedVCF,character-method	Man page
addFrequencies,ExpandedVCF,list-method	Man page
addFrequencies,ExpandedVCF,missing-method	Man page
addFrequencies-methods	Man page
addOverallFrequencies	Man page
addOverallFrequencies,ExpandedVCF-method	Man page
addOverallFrequencies-methods	Man page
addPhenoLevelFrequencies	Man page
addPhenoLevelFrequencies,ExpandedVCF-method	Man page
addPhenoLevelFrequencies-methods	Man page
alt,Genotypes-method	Man page
alt,TVTBparam-method	Man page
alt<-,Genotypes,character-method	Man page
alt<-,TVTBparam,character-method	Man page
alt<-,TVTBparam,list-method	Man page
append,VcfFilterRules,FilterRules-method	Man page
append,VcfFixedRules,FilterRules-method	Man page
append,VcfInfoRules,FilterRules-method	Man page
append,VcfVepRules,FilterRules-method	Man page
autodetectGenotypes	Man page
autodetectGenotypes,VCF-method	Man page
autodetectGenotypes-methods	Man page
bp	Man page
bp,TVTBparam-method	Man page
bp<-	Man page
bp<-,TVTBparam,BiocParallelParam-method	Man page
c,VcfFilterRules-method	Man page
c,VcfFixedRules-method	Man page
c,VcfInfoRules-method	Man page
c,VcfVepRules-method	Man page
carrier	Man page
carrier,Genotypes-method	Man page
carrier,TVTBparam-method	Man page
class:Genotypes	Man page
class:TVTBparam	Man page
class:VcfFilterRules	Man page
class:VcfFixedRules	Man page
class:VcfInfoRules	Man page
class:VcfVepRules	Man page
countGenos	Man page
countGenos,ExpandedVCF-method	Man page
countGenos-methods	Man page
dropInfo	Man page
dropInfo,VCF-method	Man page
dropInfo-methods	Man page
eval,VcfFilterRules,VCF-method	Man page
eval,VcfFixedRules,VCF-method	Man page
eval,VcfInfoRules,VCF-method	Man page
eval,VcfVepRules,VCF-method	Man page
genos	Man page
genos,Genotypes-method	Man page
genos,TVTBparam-method	Man page
genos<-	Man page
genos<-,TVTBparam,Genotypes-method	Man page
het	Man page
het,Genotypes-method	Man page
het,TVTBparam-method	Man page
het<-	Man page
het<-,Genotypes,character-method	Man page
het<-,TVTBparam,character-method	Man page
het<-,TVTBparam,list-method	Man page
initialize,Genotypes-method	Man page
initialize,TVTBparam-method	Man page
initialize,VcfFilterRules-method	Man page
initialize,VcfFixedRules-method	Man page
initialize,VcfInfoRules-method	Man page
initialize,VcfVepRules-method	Man page
maf	Man page
maf,TVTBparam-method	Man page
maf<-	Man page
maf<-,TVTBparam,character-method	Man page
pairsInfo	Man page
pairsInfo,VCF-method	Man page
pairsInfo-methods	Man page
plotInfo	Man page
plotInfo,VCF-method	Man page
plotInfo-methods	Man page
ranges	Man page
ranges,TVTBparam-method	Man page
ranges<-	Man page
ranges<-,TVTBparam,GRangesList-method	Man page
readVcf,TabixFile,TVTBparam-method	Man page
readVcf,character,TVTBparam-method	Man page
ref,Genotypes-method	Man page
ref,TVTBparam-method	Man page
ref<-,Genotypes,character-method	Man page
ref<-,TVTBparam,character-method	Man page
ref<-,TVTBparam,list-method	Man page
suffix	Man page
suffix,Genotypes-method	Man page
suffix,TVTBparam-method	Man page
svp	Man page
svp,TVTBparam-method	Man page
svp<-	Man page
svp<-,TVTBparam,ScanVcfParam-method	Man page
tSVE	Man page Source code
type,FilterRules-method	Man page
type,VcfFilterRules-method	Man page
type,VcfFixedRules-method	Man page
type,VcfInfoRules-method	Man page
type,VcfVepRules-method	Man page
variantsInSamples	Man page
variantsInSamples,ExpandedVCF-method	Man page
variantsInSamples-methods	Man page
vep	Man page
vep,FilterRules-method	Man page
vep,TVTBparam-method	Man page
vep,VcfFilterRules-method	Man page
vep,VcfFixedRules-method	Man page
vep,VcfInfoRules-method	Man page
vep,VcfVepRules-method	Man page
vep<-	Man page
vep<-,TVTBparam,character-method	Man page
vep<-,VcfFilterRules,character-method	Man page
vep<-,VcfVepRules,character-method	Man page
vepInPhenoLevel	Man page
vepInPhenoLevel,ExpandedVCF-method	Man page
vepInPhenoLevel-methods	Man page