API for kevinrue/tSVE
TVTB: The VCF Tool Box

Global functions
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
VcfBasicRules Source code
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 Source code
addCountGenos,ExpandedVCF-method Man page
addCountGenos-methods Man page
addFrequencies Man page Source code
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 Source code
addOverallFrequencies,ExpandedVCF-method Man page
addOverallFrequencies-methods Man page
addPhenoLevelFrequencies Man page Source code
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 Source code
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
checkInputsPLF Source code
checkOverallInfo Source code
checkPLFInfo Source code
checkParam Source code
checkPhenoLevel Source code
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 Source code
countGenos,ExpandedVCF-method Man page
countGenos-methods Man page
dropInfo Man page Source code
dropInfo,VCF-method Man page
dropInfo-methods Man page
dropInfoData Source code
dropInfoHeader Source code
dropVcfFilterRules Source code
eval,VcfFilterRules,VCF-method Man page
eval,VcfFixedRules,VCF-method Man page
eval,VcfInfoRules,VCF-method Man page
eval,VcfVepRules,VCF-method Man page
evalVepFilter Source code
findInfoMetricColumns Source code
geneRegionTrackFromEnsDb Source code
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 Source code
pairsInfo,VCF-method Man page
pairsInfo-methods Man page
plotInfo Man page Source code
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 Source code
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
valid.Genotypes Source code
valid.TVTBparam Source code
valid.VcfBasicRules Source code
valid.VcfFilterRules Source code
valid.VcfVepRules Source code
variantsInSamples Man page Source code
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 Source code
vepInPhenoLevel,ExpandedVCF-method Man page
vepInPhenoLevel-methods Man page
kevinrue/tSVE documentation built on Aug. 11, 2017, 4:14 p.m.