!,VAFilterResult-method	VAFilterResult-class
.VAUtil-class	VAUtil-class
c,VAFilter-method	VAFilter-class
class:PolyPhenDb	PolyPhenDb-class
class:SIFTDb	SIFTDb-class
coerce,VAFilter,FilterRules-method	VAFilter-class
cols,PolyPhenDb-method	PolyPhenDb-class
cols,SIFTDb-method	SIFTDb-class
compose	vaFilter
dbSNPFilter	vaFilter
duplicateRSID	PolyPhenDb-class
getTranscriptSeqs	getTranscriptSeqs
getTranscriptSeqs,GRanges,FaFile-method	getTranscriptSeqs
getTranscriptSeqs,GRangesList,BSgenome-method	getTranscriptSeqs
getTranscriptSeqs,GRangesList,FaFile-method	getTranscriptSeqs
globalToLocal	globalToLocal
keys,PolyPhenDb-method	PolyPhenDb-class
keys,SIFTDb-method	SIFTDb-class
locateVariants	locateVariants
locateVariants,GRanges,TranscriptDb-method	locateVariants
Logic,VAFilterResult,VAFilterResult-method	VAFilterResult-class
MatrixToSnpMatrix	MatrixToSnpMatrix
metadata,PolyPhenDb-method	PolyPhenDb-class
metadata,SIFTDb-method	SIFTDb-class
name	VAFilter-class
name,VAFilter-method	VAFilter-class
name,VAFilterResult-method	VAFilterResult-class
PolyPhen	PolyPhenDb-class
PolyPhenDb	PolyPhenDb-class
PolyPhenDb-class	PolyPhenDb-class
PolyPhenDbColumns	PolyPhenDbColumns
predictCoding	predictCoding
predictCoding,GRanges,GRangesList,ANY,character-method	predictCoding
predictCoding,GRanges,TranscriptDb,ANY,character-method	predictCoding
predictCoding,Ranges,GRangesList,ANY,character-method	predictCoding
predictCoding,Ranges,TranscriptDb,ANY,character-method	predictCoding
readVcf	readVcf
readVcf,character,ANY-method	readVcf
readVcf,character,missing-method	readVcf
readVcf,TabixFile,GRanges-method	readVcf
readVcf,TabixFile,missing-method	readVcf
readVcf,TabixFile,RangedData-method	readVcf
readVcf,TabixFile,RangesList-method	readVcf
readVcf,TabixFile,ScanVcfParam-method	readVcf
regionFilter	vaFilter
select,PolyPhenDb-method	PolyPhenDb-class
select,SIFTDb-method	SIFTDb-class
show,VAFilter-method	VAFilter-class
show,VAFilterResult-method	VAFilterResult-class
SIFT	SIFTDb-class
SIFTDb	SIFTDb-class
SIFTDb-class	SIFTDb-class
SIFTDbColumns	SIFTDbColumns
stats	VAFilterResult-class
stats,VAFilterResult-method	VAFilterResult-class
vaFilter	vaFilter
vaFilter,function-method	vaFilter
vaFilter,missing-method	vaFilter
vaFilter,VAFilter-method	VAFilter-class
VAFilter-class	VAFilter-class
VAFilterResult	VAFilterResult-class
VAFilterResult-class	VAFilterResult-class
variants	variant
