VariantFiltering-package	VariantFiltering-package
$,VariantFilteringParam-method	VariantFilteringParam-class
aaChangeType	VariantFiltering-deprecated
aaChangeType,VariantFilteringResults-method	VariantFiltering-deprecated
aaChangeType<-	VariantFiltering-deprecated
aaChangeType<-,VariantFilteringResults,character-method	VariantFiltering-deprecated
allVariants	VariantFilteringResults-class
allVariants,VariantFilteringResults-method	VariantFilteringResults-class
annoGroups	VariantFilteringResults-class
annoGroups,VariantFilteringResults-method	VariantFilteringResults-class
autosomalDominant	autosomalDominant
autosomalDominant,VariantFilteringParam-method	autosomalDominant
autosomalRecessiveHeterozygous	autosomalRecessiveHeterozygous
autosomalRecessiveHeterozygous,VariantFilteringParam-method	autosomalRecessiveHeterozygous
autosomalRecessiveHomozygous	autosomalRecessiveHomozygous
autosomalRecessiveHomozygous,VariantFilteringParam-method	autosomalRecessiveHomozygous
bamFiles	VariantFilteringResults-class
bamFiles,VariantFilteringResults-method	VariantFilteringResults-class
bamFiles<-	VariantFilteringResults-class
bamFiles<-,VariantFilteringResults,BamViews-method	VariantFilteringResults-class
bamFiles<-,VariantFilteringResults-method	VariantFilteringResults-class
browseVariants	VariantFilteringResults-class
change	VariantFilteringResults-class
change<-	VariantFilteringResults-class
change<-,CutoffsList	VariantFilteringResults-class
change<-,CutoffsList,ANY,character-method	VariantFilteringResults-class
change<-,CutoffsList,ANY,integer-method	VariantFilteringResults-class
change<-,CutoffsList,ANY,logical-method	VariantFilteringResults-class
change<-,CutoffsList,ANY,numeric-method	VariantFilteringResults-class
class:CutoffsList	VariantFilteringResults-class
class:VariantFilteringParam	VariantFilteringParam-class
class:VariantFilteringResults	VariantFilteringResults-class
conservedPositions	WeightMatrix-class
conservedPositions,WeightMatrix-method	WeightMatrix-class
cutoffs	VariantFilteringResults-class
cutoffs,VariantFilteringParam-method	VariantFilteringParam-class
cutoffs,VariantFilteringResults-method	VariantFilteringResults-class
cutoffs<-	VariantFilteringResults-class
cutoffs<-,VariantFilteringResults,CutoffsList-method	VariantFilteringResults-class
cutoffs<-,VariantFilteringResults,logical-method	VariantFilteringResults-class
cutoffs<-,VariantFilteringResults-method	VariantFilteringResults-class
CutoffsList	VariantFilteringResults-class
CutoffsList-class	VariantFilteringResults-class
dbSNPpresent	VariantFiltering-deprecated
dbSNPpresent,VariantFilteringResults-method	VariantFiltering-deprecated
dbSNPpresent<-	VariantFiltering-deprecated
dbSNPpresent<-,VariantFilteringResults,ANY-method	VariantFiltering-deprecated
dbSNPpresent<-,VariantFilteringResults-method	VariantFiltering-deprecated
deNovo	deNovo
deNovo,VariantFilteringParam-method	deNovo
downstream	VariantType-class
downstream,FiveSpliceSiteVariants-method	VariantType-class
downstream,ThreeSpliceSiteVariants-method	VariantType-class
downstream<-	VariantType-class
downstream<-,FiveSpliceSiteVariants-method	VariantType-class
downstream<-,ThreeSpliceSiteVariants-method	VariantType-class
fetchKnownVariantsByID	VariantFiltering-defunct
fetchKnownVariantsByID,MafDb-method	VariantFiltering-defunct
filteredVariants	VariantFilteringResults-class
filteredVariants,VariantFilteringResults-method	VariantFilteringResults-class
filters	VariantFilteringResults-class
filters,VariantFilteringParam-method	VariantFilteringParam-class
filters,VariantFilteringResults-method	VariantFilteringResults-class
filters<-	VariantFilteringResults-class
filters<-,VariantFilteringResults-method	VariantFilteringResults-class
filtersMetadata	VariantFilteringResults-class
filtersMetadata,VariantFilteringParam-method	VariantFilteringResults-class
filtersMetadata,VariantFilteringResults-method	VariantFilteringResults-class
FiveSpliceSiteVariants	VariantType-class
FiveSpliceSiteVariants-class	VariantType-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
length	VariantFilteringResults-class
length,VariantFilteringResults-method	VariantFilteringResults-class
MAFpop	VariantFiltering-deprecated
MAFpop,VariantFilteringResults-method	VariantFiltering-deprecated
MAFpop<-	VariantFiltering-deprecated
MAFpop<-,VariantFilteringResults,ANY,logical-method	VariantFiltering-deprecated
MAFpop<-,VariantFilteringResults,logical-method	VariantFiltering-deprecated
MAFpop<-,VariantFilteringResults-method	VariantFiltering-deprecated
maxMAF	VariantFiltering-deprecated
maxMAF,VariantFilteringResults-method	VariantFiltering-deprecated
maxMAF<-	VariantFiltering-deprecated
maxMAF<-,VariantFilteringResults,numeric-method	VariantFiltering-deprecated
minCUFC	VariantFiltering-deprecated
minCUFC,VariantFilteringResults-method	VariantFiltering-deprecated
minCUFC<-	VariantFiltering-deprecated
minCUFC<-,VariantFilteringResults,numeric-method	VariantFiltering-deprecated
minIntronLength	VariantType-class
minIntronLength,FiveSpliceSiteVariants-method	VariantType-class
minIntronLength,ThreeSpliceSiteVariants-method	VariantType-class
minIntronLength<-	VariantType-class
minIntronLength<-,FiveSpliceSiteVariants-method	VariantType-class
minIntronLength<-,ThreeSpliceSiteVariants-method	VariantType-class
minPhastCons	VariantFiltering-deprecated
minPhastCons,VariantFilteringResults-method	VariantFiltering-deprecated
minPhastCons<-	VariantFiltering-deprecated
minPhastCons<-,VariantFilteringResults,ANY-method	VariantFiltering-deprecated
minPhastCons<-,VariantFilteringResults-method	VariantFiltering-deprecated
minPhylostratum	VariantFiltering-deprecated
minPhylostratum,VariantFilteringResults-method	VariantFiltering-deprecated
minPhylostratum<-	VariantFiltering-deprecated
minPhylostratum<-,VariantFilteringResults,ANY-method	VariantFiltering-deprecated
minPhylostratum<-,VariantFilteringResults-method	VariantFiltering-deprecated
minScore3ss	VariantFiltering-deprecated
minScore3ss,VariantFilteringResults-method	VariantFiltering-deprecated
minScore3ss<-	VariantFiltering-deprecated
minScore3ss<-,VariantFilteringResults,ANY-method	VariantFiltering-deprecated
minScore3ss<-,VariantFilteringResults-method	VariantFiltering-deprecated
minScore5ss	VariantFiltering-deprecated
minScore5ss,VariantFilteringResults-method	VariantFiltering-deprecated
minScore5ss<-	VariantFiltering-deprecated
minScore5ss<-,VariantFilteringResults,ANY-method	VariantFiltering-deprecated
minScore5ss<-,VariantFilteringResults-method	VariantFiltering-deprecated
naMAF	VariantFiltering-deprecated
naMAF,VariantFilteringResults-method	VariantFiltering-deprecated
naMAF<-	VariantFiltering-deprecated
naMAF<-,VariantFilteringResults,logical-method	VariantFiltering-deprecated
names,VariantFilteringParam-method	VariantFilteringParam-class
OMIMpresent	VariantFiltering-deprecated
OMIMpresent,VariantFilteringResults-method	VariantFiltering-deprecated
OMIMpresent<-	VariantFiltering-deprecated
OMIMpresent<-,VariantFilteringResults,character-method	VariantFiltering-deprecated
OMIMpresent<-,VariantFilteringResults-method	VariantFiltering-deprecated
organism,GenePhylostrataDb-method	GenePhylostrataDb-class
param	VariantFilteringResults-class
param,VariantFilteringResults-method	VariantFilteringResults-class
plot,VariantFilteringResults,ANY-method	VariantFilteringResults-class
readAAradicalChangeMatrix	readAAradicalChangeMatrix
readWm	WeightMatrix-class
referenceGenome,VariantFilteringResults-method	VariantFilteringResults-class
reportVariants	VariantFilteringResults-class
reportVariants,VariantFilteringResults-method	VariantFilteringResults-class
resetSamples	VariantFilteringResults-class
resetSamples,VariantFilteringResults-method	VariantFilteringResults-class
samples	VariantFilteringResults-class
samples,VariantFilteringResults-method	VariantFilteringResults-class
samples<-	VariantFilteringResults-class
samples<-,VariantFilteringResults,character-method	VariantFilteringResults-class
samples<-,VariantFilteringResults-method	VariantFilteringResults-class
sequence_variant.gSOXP	VariantFilteringParam-class
show,CompressedVRangesList-method	VariantFilteringResults-class
show,FiveSpliceSiteVariants-method	VariantType-class
show,GenePhylostrataDb-method	GenePhylostrataDb-class
show,ThreeSpliceSiteVariants-method	VariantType-class
show,VariantFilteringParam-method	VariantFilteringParam-class
show,VariantFilteringResults-method	VariantFilteringResults-class
show,VariantFilteringResultsUI-method	VariantFilteringResults-class
show,WeightMatrix-method	WeightMatrix-class
softFilterMatrix,VariantFilteringResults-method	VariantFilteringResults-class
softFilterMatrix<-,VariantFilteringResults-method	VariantFilteringResults-class
sog	VariantFilteringResults-class
sog,VariantFilteringParam-method	VariantFilteringParam-class
sog,VariantFilteringResults-method	VariantFilteringResults-class
sortings	VariantFilteringResults-class
sortings,VariantFilteringResults-method	VariantFilteringResults-class
sortings<-	VariantFilteringResults-class
sortings<-,VariantFilteringResults,CutoffsList-method	VariantFilteringResults-class
spliceSiteMatricesHuman	VariantFilteringParam-class
summary,VariantFilteringResults-method	VariantFilteringResults-class
ThreeSpliceSiteVariants	VariantType-class
ThreeSpliceSiteVariants-class	VariantType-class
unrelatedIndividuals	unrelatedIndividuals
unrelatedIndividuals,VariantFilteringParam-method	unrelatedIndividuals
upstream	VariantType-class
upstream,FiveSpliceSiteVariants-method	VariantType-class
upstream,ThreeSpliceSiteVariants-method	VariantType-class
upstream<-	VariantType-class
upstream<-,FiveSpliceSiteVariants-method	VariantType-class
upstream<-,ThreeSpliceSiteVariants-method	VariantType-class
variantConsequence	VariantFiltering-deprecated
variantConsequence,VariantFilteringResults-method	VariantFiltering-deprecated
variantConsequence<-	VariantFiltering-deprecated
variantConsequence<-,VariantFilteringResults,ANY,logical-method	VariantFiltering-deprecated
variantConsequence<-,VariantFilteringResults,logical-method	VariantFiltering-deprecated
variantConsequence<-,VariantFilteringResults-method	VariantFiltering-deprecated
VariantFiltering	VariantFiltering-package
VariantFiltering-defunct	VariantFiltering-defunct
VariantFiltering-deprecated	VariantFiltering-deprecated
VariantFilteringParam	VariantFilteringParam-class
VariantFilteringParam-class	VariantFilteringParam-class
VariantFilteringResults	VariantFilteringResults-class
VariantFilteringResults-class	VariantFilteringResults-class
variantLocation	VariantFiltering-deprecated
variantLocation,VariantFilteringResults-method	VariantFiltering-deprecated
variantLocation<-	VariantFiltering-deprecated
variantLocation<-,VariantFilteringResults,ANY,logical-method	VariantFiltering-deprecated
variantLocation<-,VariantFilteringResults,logical-method	VariantFiltering-deprecated
variantLocation<-,VariantFilteringResults-method	VariantFiltering-deprecated
variantLocations	VariantFilteringParam-class
variantType	VariantFiltering-deprecated
variantType,VariantFilteringResults-method	VariantFiltering-deprecated
variantType<-	VariantFiltering-deprecated
variantType<-,VariantFilteringResults,ANY,logical-method	VariantFiltering-deprecated
variantType<-,VariantFilteringResults,logical-method	VariantFiltering-deprecated
variantType<-,VariantFilteringResults-method	VariantFiltering-deprecated
WeightMatrix	WeightMatrix-class
WeightMatrix-class	WeightMatrix-class
width,WeightMatrix-method	WeightMatrix-class
wmFilename	WeightMatrix-class
wmFilename,WeightMatrix-method	WeightMatrix-class
wmLocations	WeightMatrix-class
wmLocations,WeightMatrix-method	WeightMatrix-class
wmLocations<-	WeightMatrix-class
wmLocations<-,WeightMatrix,character-method	WeightMatrix-class
wmLocations<-,WeightMatrix-method	WeightMatrix-class
wmName	WeightMatrix-class
wmName,WeightMatrix-method	WeightMatrix-class
wmScore	WeightMatrix-class
wmScore,character,character-method	WeightMatrix-class
wmScore,character,DNAStringSet-method	WeightMatrix-class
wmScore,WeightMatrix,character-method	WeightMatrix-class
wmScore,WeightMatrix,DNAStringSet-method	WeightMatrix-class
wmStrictLocations	WeightMatrix-class
wmStrictLocations,WeightMatrix-method	WeightMatrix-class
wmStrictLocations<-	WeightMatrix-class
wmStrictLocations<-,WeightMatrix,logical-method	WeightMatrix-class
wmStrictLocations<-,WeightMatrix-method	WeightMatrix-class
xLinked	xLinked
xLinked,VariantFilteringParam-method	xLinked
