VariantFiltering-package	VariantFiltering-package
$,VariantFilteringParam-method	VariantFilteringParam-class
aaChangeType	VariantFilteringResults-class
aaChangeType,VariantFilteringResults-method	VariantFilteringResults-class
aaChangeType<-	VariantFilteringResults-class
aaChangeType<-,VariantFilteringResults,character-method	VariantFilteringResults-class
allInheritanceModels	allInheritanceModels
allInheritanceModels,VariantFilteringParam-method	allInheritanceModels
allVariants	VariantFilteringResults-class
allVariants,VariantFilteringResults-method	VariantFilteringResults-class
annotateVariants	MafDb-class
annotateVariants,GenePhylostrataDb-method	GenePhylostrataDb-class
annotateVariants,MafDb-method	MafDb-class
annotateVariants,OrgDb-method	MafDb-class
annotateVariants,PhastConsDb-method	PhastConsDb-class
annotateVariants,PolyPhenDb-method	MafDb-class
annotateVariants,PROVEANDb-method	MafDb-class
annotateVariants,SNPlocs-method	MafDb-class
annotateVariants,TxDb-method	MafDb-class
autosomalDominant	autosomalDominant
autosomalDominant,VariantFilteringParam-method	autosomalDominant
autosomalRecessiveHeterozygous	autosomalRecessiveHeterozygous
autosomalRecessiveHeterozygous,VariantFilteringParam-method	autosomalRecessiveHeterozygous
autosomalRecessiveHomozygous	autosomalRecessiveHomozygous
autosomalRecessiveHomozygous,VariantFilteringParam-method	autosomalRecessiveHomozygous
class:VariantFilteringParam	VariantFilteringParam-class
class:VariantFilteringResults	VariantFilteringResults-class
class:VariantFilteringResultsAIM	VariantFilteringResults-class
class:VariantFilteringResultsUI	VariantFilteringResults-class
codeAF2RAW	MafDb-class
columns	MafDb-class
columns,MafDb-method	MafDb-class
conservedPositions	WeightMatrix-class
conservedPositions,WeightMatrix-method	WeightMatrix-class
dbSNPpresent	VariantFilteringResults-class
dbSNPpresent,VariantFilteringResults-method	VariantFilteringResults-class
dbSNPpresent<-	VariantFilteringResults-class
dbSNPpresent<-,VariantFilteringResults,ANY-method	VariantFilteringResults-class
dbSNPpresent<-,VariantFilteringResults-method	VariantFilteringResults-class
decodeRAW2AF	MafDb-class
deNovo	deNovo
deNovo,VariantFilteringParam-method	deNovo
fetchKnownVariantsByID	MafDb-class
fetchKnownVariantsByID,MafDb-method	MafDb-class
filteredVariants	VariantFilteringResults-class
filteredVariants,VariantFilteringResults-method	VariantFilteringResults-class
filteredVariants,VariantFilteringResultsAIM-method	VariantFilteringResults-class
filteredVariants,VariantFilteringResultsUI-method	VariantFilteringResults-class
genePhylostrata	GenePhylostrataDb-class
genePhylostrata,GenePhylostrataDb-method	GenePhylostrataDb-class
GenePhylostrataDb	GenePhylostrataDb-class
GenePhylostrataDb-class	GenePhylostrataDb-class
genePhylostratum	GenePhylostrataDb-class
genePhylostratum,GenePhylostrataDb,character-method	GenePhylostrataDb-class
genePhylostratum,GenePhylostrataDb,missing-method	GenePhylostrataDb-class
genePhylostratum,GenePhylostrataDb-method	GenePhylostrataDb-class
humanGenesPhylostrata	GenePhylostrataDb-class
inheritanceModel	VariantFilteringResults-class
inheritanceModel,VariantFilteringResults-method	VariantFilteringResults-class
keys	MafDb-class
keys,MafDb-method	MafDb-class
keytypes	MafDb-class
keytypes,MafDb-method	MafDb-class
knownVariantsMAFcols	MafDb-class
knownVariantsMAFcols,MafDb-method	MafDb-class
MafDb	MafDb-class
MafDb-class	MafDb-class
MAFpop	VariantFilteringResults-class
MAFpop,VariantFilteringResults-method	VariantFilteringResults-class
MAFpop<-	VariantFilteringResults-class
MAFpop<-,VariantFilteringResults,ANY,logical-method	VariantFilteringResults-class
MAFpop<-,VariantFilteringResults,logical-method	VariantFilteringResults-class
MAFpop<-,VariantFilteringResults-method	VariantFilteringResults-class
maxMAF	VariantFilteringResults-class
maxMAF,VariantFilteringResults-method	VariantFilteringResults-class
maxMAF<-	VariantFilteringResults-class
maxMAF<-,VariantFilteringResults,numeric-method	VariantFilteringResults-class
minCRYP3ss	VariantFilteringResults-class
minCRYP3ss,VariantFilteringResults-method	VariantFilteringResults-class
minCRYP3ss<-	VariantFilteringResults-class
minCRYP3ss<-,VariantFilteringResults,ANY-method	VariantFilteringResults-class
minCRYP3ss<-,VariantFilteringResults-method	VariantFilteringResults-class
minCRYP5ss	VariantFilteringResults-class
minCRYP5ss,VariantFilteringResults-method	VariantFilteringResults-class
minCRYP5ss<-	VariantFilteringResults-class
minCRYP5ss<-,VariantFilteringResults,ANY-method	VariantFilteringResults-class
minCRYP5ss<-,VariantFilteringResults-method	VariantFilteringResults-class
minPhastCons	VariantFilteringResults-class
minPhastCons,VariantFilteringResults-method	VariantFilteringResults-class
minPhastCons<-	VariantFilteringResults-class
minPhastCons<-,VariantFilteringResults,ANY-method	VariantFilteringResults-class
minPhastCons<-,VariantFilteringResults-method	VariantFilteringResults-class
minPhylostratum	VariantFilteringResults-class
minPhylostratum,VariantFilteringResults-method	VariantFilteringResults-class
minPhylostratum<-	VariantFilteringResults-class
minPhylostratum<-,VariantFilteringResults,ANY-method	VariantFilteringResults-class
minPhylostratum<-,VariantFilteringResults-method	VariantFilteringResults-class
naMAF	VariantFilteringResults-class
naMAF,VariantFilteringResults-method	VariantFilteringResults-class
naMAF<-	VariantFilteringResults-class
naMAF<-,VariantFilteringResults,logical-method	VariantFilteringResults-class
names,VariantFilteringParam-method	VariantFilteringParam-class
OMIMpresent	VariantFilteringResults-class
OMIMpresent,VariantFilteringResults-method	VariantFilteringResults-class
OMIMpresent<-	VariantFilteringResults-class
OMIMpresent<-,VariantFilteringResults,character-method	VariantFilteringResults-class
OMIMpresent<-,VariantFilteringResults-method	VariantFilteringResults-class
organism,GenePhylostrataDb-method	GenePhylostrataDb-class
organism,PhastConsDb-method	PhastConsDb-class
param	VariantFilteringResults-class
param,VariantFilteringResults-method	VariantFilteringResults-class
PhastConsDb	PhastConsDb-class
PhastConsDb-class	PhastConsDb-class
provider,PhastConsDb-method	PhastConsDb-class
providerVersion,PhastConsDb-method	PhastConsDb-class
readAAradicalChangeMatrix	readAAradicalChangeMatrix
readWm	WeightMatrix-class
referenceGenome,PhastConsDb-method	PhastConsDb-class
reportVariants	VariantFilteringResults-class
reportVariants,VariantFilteringResults-method	VariantFilteringResults-class
reportVariants,VariantFilteringResultsAIM-method	VariantFilteringResults-class
reportVariants,VariantFilteringResultsUI-method	VariantFilteringResults-class
scores	PhastConsDb-class
scores,PhastConsDb,GRanges-method	PhastConsDb-class
select	MafDb-class
select,MafDb-method	MafDb-class
selectIndividual	VariantFilteringResults-class
selectIndividual,VariantFilteringResultsAIM-method	VariantFilteringResults-class
selectIndividual,VariantFilteringResultsUI-method	VariantFilteringResults-class
selectIndividual<-	VariantFilteringResults-class
selectIndividual<-,VariantFilteringResultsAIM,character-method	VariantFilteringResults-class
selectIndividual<-,VariantFilteringResultsAIM-method	VariantFilteringResults-class
selectIndividual<-,VariantFilteringResultsUI,character-method	VariantFilteringResults-class
selectIndividual<-,VariantFilteringResultsUI-method	VariantFilteringResults-class
seqinfo,PhastConsDb-method	PhastConsDb-class
seqlengths,PhastConsDb-method	PhastConsDb-class
seqnames,PhastConsDb-method	PhastConsDb-class
show,GenePhylostrataDb-method	GenePhylostrataDb-class
show,PhastConsDb-method	PhastConsDb-class
show,VariantFilteringParam-method	VariantFilteringParam-class
show,VariantFilteringResults-method	VariantFilteringResults-class
show,VariantFilteringResultsAIM-method	VariantFilteringResults-class
show,VariantFilteringResultsUI-method	VariantFilteringResults-class
show,WeightMatrix-method	WeightMatrix-class
unrelatedIndividuals	unrelatedIndividuals
unrelatedIndividuals,VariantFilteringParam-method	unrelatedIndividuals
VariantFiltering	VariantFiltering-package
VariantFilteringParam	VariantFilteringParam-class
VariantFilteringParam,character-method	VariantFilteringParam-class
VariantFilteringParam-class	VariantFilteringParam-class
VariantFilteringResults	VariantFilteringResults-class
VariantFilteringResults-class	VariantFilteringResults-class
VariantFilteringResultsAIM	VariantFilteringResults-class
VariantFilteringResultsAIM-class	VariantFilteringResults-class
VariantFilteringResultsUI	VariantFilteringResults-class
VariantFilteringResultsUI-class	VariantFilteringResults-class
variantType	VariantFilteringResults-class
variantType,VariantFilteringResults-method	VariantFilteringResults-class
variantType<-	VariantFilteringResults-class
variantType<-,VariantFilteringResults,character-method	VariantFilteringResults-class
WeightMatrix	WeightMatrix-class
WeightMatrix-class	WeightMatrix-class
width,WeightMatrix-method	WeightMatrix-class
wmAcceptorSites	WeightMatrix-class
wmDonorSites	WeightMatrix-class
wmScore	WeightMatrix-class
wmScore,WeightMatrix,character-method	WeightMatrix-class
wmScore,WeightMatrix,DNAStringSet-method	WeightMatrix-class
xLinked	xLinked
xLinked,VariantFilteringParam-method	xLinked
