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