VariantFiltering-package	VariantFiltering-package
$,MafDb2-method	MafDb2-class
$,VariantFilteringParam-method	VariantFilteringParam-class
aaChangeType	VariantFilteringResults-class
aaChangeType,VariantFilteringResults-method	VariantFilteringResults-class
aaChangeType<-	VariantFilteringResults-class
aaChangeType<-,VariantFilteringResults,character-method	VariantFilteringResults-class
allVariants	VariantFilteringResults-class
allVariants,VariantFilteringResults-method	VariantFilteringResults-class
annotateVariants	MafDb-class
annotateVariants,GenePhylostrataDb-method	GenePhylostrataDb-class
annotateVariants,MafDb-method	MafDb-class
annotateVariants,MafDb2-method	MafDb2-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
annotateVariants,XtraSNPlocs-method	MafDb-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
class:VariantFilteringParam	VariantFilteringParam-class
class:VariantFilteringResults	VariantFilteringResults-class
codeAF2RAW	MafDb-class
columns	MafDb-class
columns,MafDb-method	MafDb-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-method	VariantFilteringResults-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
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
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
keys	MafDb-class
keys,MafDb-method	MafDb-class
keytypes	MafDb-class
keytypes,MafDb-method	MafDb-class
knownVariantsMAFcols	MafDb-class
knownVariantsMAFcols,MafDb-method	MafDb-class
length	VariantFilteringResults-class
length,VariantFilteringResults-method	VariantFilteringResults-class
mafById	MafDb2-class
mafById,MafDb2-method	MafDb2-class
mafByOverlaps	MafDb2-class
mafByOverlaps,MafDb2-method	MafDb2-class
MafDb	MafDb-class
MafDb-class	MafDb-class
MafDb2	MafDb2-class
MafDb2-class	MafDb2-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
minCUFC	VariantFilteringResults-class
minCUFC,VariantFilteringResults-method	VariantFilteringResults-class
minCUFC<-	VariantFilteringResults-class
minCUFC<-,VariantFilteringResults,numeric-method	VariantFilteringResults-class
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	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
minScore3ss	VariantFilteringResults-class
minScore3ss,VariantFilteringResults-method	VariantFilteringResults-class
minScore3ss<-	VariantFilteringResults-class
minScore3ss<-,VariantFilteringResults,ANY-method	VariantFilteringResults-class
minScore3ss<-,VariantFilteringResults-method	VariantFilteringResults-class
minScore5ss	VariantFilteringResults-class
minScore5ss,VariantFilteringResults-method	VariantFilteringResults-class
minScore5ss<-	VariantFilteringResults-class
minScore5ss<-,VariantFilteringResults,ANY-method	VariantFilteringResults-class
minScore5ss<-,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,MafDb2-method	MafDb2-class
organism,PhastConsDb-method	PhastConsDb-class
param	VariantFilteringResults-class
param,VariantFilteringResults-method	VariantFilteringResults-class
PhastConsDb	PhastConsDb-class
PhastConsDb-class	PhastConsDb-class
plot,VariantFilteringResults,ANY-method	VariantFilteringResults-class
populations	MafDb2-class
populations,MafDb2-method	MafDb2-class
provider,MafDb2-method	MafDb2-class
provider,PhastConsDb-method	PhastConsDb-class
providerVersion,MafDb2-method	MafDb2-class
providerVersion,PhastConsDb-method	PhastConsDb-class
readAAradicalChangeMatrix	readAAradicalChangeMatrix
readWm	WeightMatrix-class
referenceGenome,MafDb2-method	MafDb2-class
referenceGenome,PhastConsDb-method	PhastConsDb-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
scores	PhastConsDb-class
scores,PhastConsDb,GRanges-method	PhastConsDb-class
select	MafDb-class
select,MafDb-method	MafDb-class
seqinfo,MafDb2-method	MafDb2-class
seqinfo,PhastConsDb-method	PhastConsDb-class
seqlengths,MafDb2-method	MafDb2-class
seqlengths,PhastConsDb-method	PhastConsDb-class
seqlevelsStyle,MafDb2-method	MafDb2-class
seqlevelsStyle,PhastConsDb-method	PhastConsDb-class
seqnames,MafDb2-method	MafDb2-class
seqnames,PhastConsDb-method	PhastConsDb-class
sequence_variant.gSOXP	VariantFilteringParam-class
show,CompressedVRangesList-method	VariantFilteringResults-class
show,FiveSpliceSiteVariants-method	VariantType-class
show,GenePhylostrataDb-method	GenePhylostrataDb-class
show,MafDb2-method	MafDb2-class
show,PhastConsDb-method	PhastConsDb-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
snpid2maf	MafDb-class
snpid2maf,MafDb-method	MafDb-class
softFilterMatrix,VariantFilteringResults-method	VariantFilteringResults-class
softFilterMatrix<-,VariantFilteringResults-method	VariantFilteringResults-class
sog	VariantFilteringResults-class
sog,VariantFilteringParam-method	VariantFilteringParam-class
sog,VariantFilteringResults-method	VariantFilteringResults-class
spliceSiteMatricesHsapiens	VariantFilteringParam-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	VariantFilteringResults-class
variantConsequence,VariantFilteringResults-method	VariantFilteringResults-class
variantConsequence<-	VariantFilteringResults-class
variantConsequence<-,VariantFilteringResults,ANY,logical-method	VariantFilteringResults-class
variantConsequence<-,VariantFilteringResults,logical-method	VariantFilteringResults-class
variantConsequence<-,VariantFilteringResults-method	VariantFilteringResults-class
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	VariantFilteringResults-class
variantLocation,VariantFilteringResults-method	VariantFilteringResults-class
variantLocation<-	VariantFilteringResults-class
variantLocation<-,VariantFilteringResults,ANY,logical-method	VariantFilteringResults-class
variantLocation<-,VariantFilteringResults,logical-method	VariantFilteringResults-class
variantLocation<-,VariantFilteringResults-method	VariantFilteringResults-class
variantType	VariantFilteringResults-class
variantType,VariantFilteringResults-method	VariantFilteringResults-class
variantType<-	VariantFilteringResults-class
variantType<-,VariantFilteringResults,ANY,logical-method	VariantFilteringResults-class
variantType<-,VariantFilteringResults,logical-method	VariantFilteringResults-class
variantType<-,VariantFilteringResults-method	VariantFilteringResults-class
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
