TVTB-package	TVTB-package
aaf	TVTBParam-class
aaf,TVTBparam-method	TVTBParam-class
aaf<-	TVTBParam-class
aaf<-,TVTBparam,character-method	TVTBParam-class
addCountGenos	addCountGenos-methods
addCountGenos,ExpandedVCF-method	addCountGenos-methods
addCountGenos-methods	addCountGenos-methods
addFrequencies	addFrequencies-methods
addFrequencies,ExpandedVCF,character-method	addFrequencies-methods
addFrequencies,ExpandedVCF,list-method	addFrequencies-methods
addFrequencies,ExpandedVCF,missing-method	addFrequencies-methods
addFrequencies-methods	addFrequencies-methods
addOverallFrequencies	addOverallFrequencies-methods
addOverallFrequencies,ExpandedVCF-method	addOverallFrequencies-methods
addOverallFrequencies-methods	addOverallFrequencies-methods
addPhenoLevelFrequencies	addPhenoLevelFrequencies-methods
addPhenoLevelFrequencies,ExpandedVCF-method	addPhenoLevelFrequencies-methods
addPhenoLevelFrequencies-methods	addPhenoLevelFrequencies-methods
alt,Genotypes-method	Genotypes-class
alt,TVTBparam-method	TVTBParam-class
alt<-,Genotypes,character-method	Genotypes-class
alt<-,TVTBparam,character-method	TVTBParam-class
alt<-,TVTBparam,list-method	TVTBParam-class
append,VcfFilterRules,FilterRules-method	VcfFilterRules-class
append,VcfFixedRules,FilterRules-method	VcfBasicRules-class
append,VcfInfoRules,FilterRules-method	VcfBasicRules-class
append,VcfVepRules,FilterRules-method	VcfBasicRules-class
autodetectGenotypes	autodetectGenotypes
autodetectGenotypes,VCF-method	autodetectGenotypes
autodetectGenotypes-methods	autodetectGenotypes
bp	TVTBParam-class
bp,TVTBparam-method	TVTBParam-class
bp<-	TVTBParam-class
bp<-,TVTBparam,BiocParallelParam-method	TVTBParam-class
c,VcfFilterRules-method	VcfFilterRules-class
c,VcfFixedRules-method	VcfBasicRules-class
c,VcfInfoRules-method	VcfBasicRules-class
c,VcfVepRules-method	VcfBasicRules-class
carrier	Genotypes-class
carrier,Genotypes-method	Genotypes-class
carrier,TVTBparam-method	TVTBParam-class
class:Genotypes	Genotypes-class
class:TVTBparam	TVTBParam-class
class:VcfFilterRules	VcfFilterRules-class
class:VcfFixedRules	VcfBasicRules-class
class:VcfInfoRules	VcfBasicRules-class
class:VcfVepRules	VcfBasicRules-class
countGenos	countGenos-methods
countGenos,ExpandedVCF-method	countGenos-methods
countGenos-methods	countGenos-methods
dropInfo	dropInfo-methods
dropInfo,VCF-method	dropInfo-methods
dropInfo-methods	dropInfo-methods
eval,VcfFilterRules,VCF-method	VcfFilterRules-class
eval,VcfFixedRules,VCF-method	VcfBasicRules-class
eval,VcfInfoRules,VCF-method	VcfBasicRules-class
eval,VcfVepRules,VCF-method	VcfBasicRules-class
genos	Genotypes-class
genos,Genotypes-method	Genotypes-class
genos,TVTBparam-method	TVTBParam-class
genos<-	TVTBParam-class
genos<-,TVTBparam,Genotypes-method	TVTBParam-class
Genotypes	Genotypes-class
Genotypes-class	Genotypes-class
Genotypes-methods	Genotypes-class
het	Genotypes-class
het,Genotypes-method	Genotypes-class
het,TVTBparam-method	TVTBParam-class
het<-	Genotypes-class
het<-,Genotypes,character-method	Genotypes-class
het<-,TVTBparam,character-method	TVTBParam-class
het<-,TVTBparam,list-method	TVTBParam-class
initialize,Genotypes-method	Genotypes-class
initialize,TVTBparam-method	TVTBParam-class
initialize,VcfFilterRules-method	VcfFilterRules-class
initialize,VcfFixedRules-method	VcfBasicRules-class
initialize,VcfInfoRules-method	VcfBasicRules-class
initialize,VcfVepRules-method	VcfBasicRules-class
maf	TVTBParam-class
maf,TVTBparam-method	TVTBParam-class
maf<-	TVTBParam-class
maf<-,TVTBparam,character-method	TVTBParam-class
pairsInfo	pairsInfo-methods
pairsInfo,VCF-method	pairsInfo-methods
pairsInfo-methods	pairsInfo-methods
parseCSQToGRanges	parseCSQToGRanges
parseCSQToGRanges,VCF-method	parseCSQToGRanges
plotInfo	plotInfo-methods
plotInfo,VCF-method	plotInfo-methods
plotInfo-methods	plotInfo-methods
ranges	TVTBParam-class
ranges,TVTBparam-method	TVTBParam-class
ranges<-	TVTBParam-class
ranges<-,TVTBparam,GRangesList-method	TVTBParam-class
readVcf,character,TVTBparam-method	readVcf-methods
readVcf,TabixFile,TVTBparam-method	readVcf-methods
ref,Genotypes-method	Genotypes-class
ref,TVTBparam-method	TVTBParam-class
ref<-,Genotypes,character-method	Genotypes-class
ref<-,TVTBparam,character-method	TVTBParam-class
ref<-,TVTBparam,list-method	TVTBParam-class
suffix	Genotypes-class
suffix,Genotypes-method	Genotypes-class
suffix,TVTBparam-method	TVTBParam-class
svp	TVTBParam-class
svp,TVTBparam-method	TVTBParam-class
svp<-	TVTBParam-class
svp<-,TVTBparam,ScanVcfParam-method	TVTBParam-class
tSVE	tSVE
TVTBparam	TVTBParam-class
TVTBparam-class	TVTBParam-class
TVTBparam-methods	TVTBParam-class
type,FilterRules-method	VcfBasicRules-class
type,VcfFilterRules-method	VcfFilterRules-class
type,VcfFixedRules-method	VcfBasicRules-class
type,VcfInfoRules-method	VcfBasicRules-class
type,VcfVepRules-method	VcfBasicRules-class
variantsInSamples	variantsInSamples-methods
variantsInSamples,ExpandedVCF-method	variantsInSamples-methods
variantsInSamples-methods	variantsInSamples-methods
VcfFilterRules	VcfFilterRules-class
VcfFilterRules-class	VcfFilterRules-class
VcfFixedRules	VcfBasicRules-class
VcfFixedRules-class	VcfBasicRules-class
VcfInfoRules	VcfBasicRules-class
VcfInfoRules-class	VcfBasicRules-class
VcfVepRules	VcfBasicRules-class
VcfVepRules-class	VcfBasicRules-class
vep	TVTBParam-class
vep,FilterRules-method	VcfBasicRules-class
vep,TVTBparam-method	TVTBParam-class
vep,VcfFilterRules-method	VcfFilterRules-class
vep,VcfFixedRules-method	VcfBasicRules-class
vep,VcfInfoRules-method	VcfBasicRules-class
vep,VcfVepRules-method	VcfBasicRules-class
vep<-	TVTBParam-class
vep<-,TVTBparam,character-method	TVTBParam-class
vep<-,VcfFilterRules,character-method	VcfFilterRules-class
vep<-,VcfVepRules,character-method	VcfBasicRules-class
vepInPhenoLevel	vepInPhenoLevel-methods
vepInPhenoLevel,ExpandedVCF-method	vepInPhenoLevel-methods
vepInPhenoLevel-methods	vepInPhenoLevel-methods
[,VcfFilterRules,ANY,ANY,ANY-method	VcfFilterRules-class
[,VcfFilterRules,ANY,ANY,logical-method	VcfFilterRules-class
[,VcfFilterRules,ANY,ANY,missing-method	VcfFilterRules-class
[,VcfFixedRules,ANY,ANY-method	VcfBasicRules-class
[,VcfInfoRules,ANY,ANY-method	VcfBasicRules-class
[,VcfVepRules,ANY,ANY-method	VcfBasicRules-class
[<-,VcfFilterRules,numeric,missing,VcfFilterRules-method	VcfFilterRules-class
[<-,VcfFilterRules,numeric,missing,VcfFixedRules-method	VcfFilterRules-class
[<-,VcfFilterRules,numeric,missing,VcfInfoRules-method	VcfFilterRules-class
[<-,VcfFilterRules,numeric,missing,VcfVepRules-method	VcfFilterRules-class
[<-,VcfFixedRules,numeric,missing,VcfFixedRules-method	VcfBasicRules-class
[<-,VcfInfoRules,numeric,missing,VcfInfoRules-method	VcfBasicRules-class
[<-,VcfVepRules,numeric,missing,VcfVepRules-method	VcfBasicRules-class
[[,VcfFilterRules,ANY,ANY-method	VcfFilterRules-class
[[,VcfFixedRules,ANY,ANY-method	VcfBasicRules-class
[[,VcfInfoRules,ANY,ANY-method	VcfBasicRules-class
[[,VcfVepRules,ANY,ANY-method	VcfBasicRules-class
[[<-,VcfFilterRules,ANY,ANY-method	VcfFilterRules-class
[[<-,VcfFixedRules,ANY,ANY-method	VcfBasicRules-class
[[<-,VcfInfoRules,ANY,ANY-method	VcfBasicRules-class
[[<-,VcfVepRules,ANY,ANY-method	VcfBasicRules-class
