!,VAFilterResult-method	VAFilterResult-class
.VAUtil-class	VAUtil-class
AllVariants	VariantType-class
AllVariants-class	VariantType-class
alt	VCF-class
alt,VCF-method	VCF-class
alt<-	VCF-class
alt<-,VCF,CharacterList-method	VCF-class
alt<-,VCF,DNAStringSetList-method	VCF-class
class:PolyPhenDb	PolyPhenDb-class
class:SIFTDb	SIFTDb-class
class:VAFilter	VAFilter-class
CodingVariants	VariantType-class
CodingVariants-class	VariantType-class
cols,PolyPhenDb-method	PolyPhenDb-class
cols,SIFTDb-method	SIFTDb-class
compose	VAFilter-class
contig	VCFHeader-class
contig,VCFHeader-method	VCFHeader-class
dbSNPFilter	VAFilter-class
duplicateRSID	PolyPhenDb-class
filt	VCF-class
filt,VCF-method	VCF-class
filt<-	VCF-class
filt<-,VCF,character-method	VCF-class
FiveUTRVariants	VariantType-class
FiveUTRVariants-class	VariantType-class
fixed	VCF-class
fixed,VCF-method	VCF-class
fixed,VCFHeader-method	VCFHeader-class
fixed<-	VCF-class
fixed<-,VCF,DataFrame-method	VCF-class
geno	VCF-class
geno,VCF-method	VCF-class
geno,VCFHeader-method	VCFHeader-class
geno<-	VCF-class
geno<-,VCF,character,matrix-method	VCF-class
geno<-,VCF,missing,SimpleList-method	VCF-class
geno<-,VCF,numeric,matrix-method	VCF-class
genome,VCF-method	VCF-class
getTranscriptSeqs	getTranscriptSeqs
getTranscriptSeqs,GRanges,FaFile-method	getTranscriptSeqs
getTranscriptSeqs,GRangesList,BSgenome-method	getTranscriptSeqs
getTranscriptSeqs,GRangesList,FaFile-method	getTranscriptSeqs
globalToLocal	globalToLocal
header	VCFHeader-class
header,VCFHeader-method	VCFHeader-class
info	VCF-class
info,VCF-method	VCF-class
info,VCFHeader-method	VCFHeader-class
info<-	VCF-class
info<-,VCF,DataFrame-method	VCF-class
IntergenicVariants	VariantType-class
IntergenicVariants-class	VariantType-class
IntronVariants	VariantType-class
IntronVariants-class	VariantType-class
keepSeqlevels,VCF,character-method	VCF-class
keys,PolyPhenDb-method	PolyPhenDb-class
keys,SIFTDb-method	SIFTDb-class
locateVariants	locateVariants
locateVariants,GRanges,GRangesList,AllVariants-method	locateVariants
locateVariants,GRanges,GRangesList,ANY-method	locateVariants
locateVariants,GRanges,GRangesList,CodingVariants-method	locateVariants
locateVariants,GRanges,GRangesList,FiveUTRVariants-method	locateVariants
locateVariants,GRanges,GRangesList,IntergenicVariants-method	locateVariants
locateVariants,GRanges,GRangesList,IntronVariants-method	locateVariants
locateVariants,GRanges,GRangesList,SpliceSiteVariants-method	locateVariants
locateVariants,GRanges,GRangesList,ThreeUTRVariants-method	locateVariants
locateVariants,GRanges,TranscriptDb,AllVariants-method	locateVariants
locateVariants,GRanges,TranscriptDb,ANY-method	locateVariants
locateVariants,GRanges,TranscriptDb,CodingVariants-method	locateVariants
locateVariants,GRanges,TranscriptDb,FiveUTRVariants-method	locateVariants
locateVariants,GRanges,TranscriptDb,IntergenicVariants-method	locateVariants
locateVariants,GRanges,TranscriptDb,IntronVariants-method	locateVariants
locateVariants,GRanges,TranscriptDb,SpliceSiteVariants-method	locateVariants
locateVariants,GRanges,TranscriptDb,ThreeUTRVariants-method	locateVariants
locateVariants,Ranges,GRangesList,ANY-method	locateVariants
locateVariants,Ranges,TranscriptDb,ANY-method	locateVariants
locateVariants,VCF,GRangesList,ANY-method	locateVariants
locateVariants,VCF,TranscriptDb,ANY-method	locateVariants
Logic,VAFilterResult,VAFilterResult-method	VAFilterResult-class
MatrixToSnpMatrix	MatrixToSnpMatrix
MatrixToSnpMatrix,matrix,DNAStringSet,DNAStringSetList-method	MatrixToSnpMatrix
meta	VCFHeader-class
meta,VCFHeader-method	VCFHeader-class
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,TranscriptDb,ANY,DNAStringSet-method	predictCoding
predictCoding,Ranges,TranscriptDb,ANY,DNAStringSet-method	predictCoding
predictCoding,VCF,TranscriptDb,ANY,missing-method	predictCoding
qual	VCF-class
qual,VCF-method	VCF-class
qual<-	VCF-class
qual<-,VCF,integer-method	VCF-class
readVcf	readVcf
readVcf,character,character,missing-method	readVcf
readVcf,character,character,ScanVcfParam-method	readVcf
readVcf,character,missing,missing-method	readVcf
readVcf,TabixFile,character,GRanges-method	readVcf
readVcf,TabixFile,character,missing-method	readVcf
readVcf,TabixFile,character,RangedData-method	readVcf
readVcf,TabixFile,character,RangesList-method	readVcf
readVcf,TabixFile,character,ScanVcfParam-method	readVcf
readVcfLongForm	readVcfLongForm
readVcfLongForm,character,character,missing-method	readVcfLongForm
readVcfLongForm,character,character,ScanVcfParam-method	readVcfLongForm
readVcfLongForm,character,missing,missing-method	readVcfLongForm
readVcfLongForm,TabixFile,character,GRanges-method	readVcfLongForm
readVcfLongForm,TabixFile,character,missing-method	readVcfLongForm
readVcfLongForm,TabixFile,character,RangedData-method	readVcfLongForm
readVcfLongForm,TabixFile,character,RangesList-method	readVcfLongForm
readVcfLongForm,TabixFile,character,ScanVcfParam-method	readVcfLongForm
ref	VCF-class
ref,VCF-method	VCF-class
ref<-	VCF-class
ref<-,VCF,DNAStringSet-method	VCF-class
reference	VCFHeader-class
reference,VCFHeader-method	VCFHeader-class
refLocsToLocalLocs	refLocsToLocalLocs
refLocsToLocalLocs,GRanges,missing,GRangesList-method	refLocsToLocalLocs
refLocsToLocalLocs,GRanges,TranscriptDb,missing-method	refLocsToLocalLocs
regionFilter	VAFilter-class
renameSeqlevels,VCF,character-method	VCF-class
samples	VCFHeader-class
samples,VCFHeader-method	VCFHeader-class
scanVcf	scanVcf
scanVcf,character,missing-method	scanVcf
scanVcf,character,ScanVcfParam-method	scanVcf
scanVcf,connection,missing-method	scanVcf
scanVcf,TabixFile,GRanges-method	scanVcf
scanVcf,TabixFile,missing-method	scanVcf
scanVcf,TabixFile,RangedData-method	scanVcf
scanVcf,TabixFile,RangesList-method	scanVcf
scanVcf,TabixFile,ScanVcfParam-method	scanVcf
scanVcfHeader	scanVcf
scanVcfHeader,character-method	scanVcf
scanVcfHeader,TabixFile-method	scanVcf
ScanVcfParam	ScanVcfParam-class
ScanVcfParam,ANY-method	ScanVcfParam-class
ScanVcfParam,missing-method	ScanVcfParam-class
ScanVcfParam-class	ScanVcfParam-class
select,PolyPhenDb-method	PolyPhenDb-class
select,SIFTDb-method	SIFTDb-class
seqlevels,VCF-method	VCF-class
show,VAFilter-method	VAFilter-class
show,VAFilterResult-method	VAFilterResult-class
show,VariantType-method	VariantType-class
show,VCF-method	VCF-class
show,VCFHeader-method	VCFHeader-class
SIFT	SIFTDb-class
SIFTDb	SIFTDb-class
SIFTDb-class	SIFTDb-class
SIFTDbColumns	SIFTDbColumns
SpliceSiteVariants	VariantType-class
SpliceSiteVariants-class	VariantType-class
stats	VAFilterResult-class
stats,VAFilterResult-method	VAFilterResult-class
ThreeUTRVariants	VariantType-class
ThreeUTRVariants-class	VariantType-class
VAFilter	VAFilter-class
vaFilter	VAFilter-class
vaFilter,function-method	VAFilter-class
vaFilter,missing-method	VAFilter-class
vaFilter,VAFilter-method	VAFilter-class
VAFilter-class	VAFilter-class
VAFilterResult	VAFilterResult-class
VAFilterResult-class	VAFilterResult-class
VariantType-class	VariantType-class
VCF	VCF-class
VCF-class	VCF-class
vcfFixed	ScanVcfParam-class
vcfGeno	ScanVcfParam-class
VCFHeader	VCFHeader-class
VCFHeader-class	VCFHeader-class
vcfInfo	ScanVcfParam-class
vcfTrimEmpty	ScanVcfParam-class
vcfWhich	ScanVcfParam-class
writeVcf	writeVcf
writeVcf,VCF,character-method	writeVcf
[,VCF,ANY,ANY,ANY-method	VCF-class
[,VCF-method	VCF-class
[<-,VCF,ANY,ANY,VCF-method	VCF-class
