AllVariants	VariantType-class
AllVariants-class	VariantType-class
alt	VCF-class
alt,VCF-method	VCF-class
alt<-	VCF-class
alt<-,CollapsedVCF,CharacterList-method	VCF-class
alt<-,CollapsedVCF,DNAStringSetList-method	VCF-class
alt<-,ExpandedVCF,character-method	VCF-class
alt<-,ExpandedVCF,DNAStringSet-method	VCF-class
cbind,VCF-method	VCF-class
class:CollapsedVCF	VCF-class
class:ExpandedVCF	VCF-class
class:PolyPhenDb	PolyPhenDb-class
class:SIFTDb	SIFTDb-class
class:VCF	VCF-class
CodingVariants	VariantType-class
CodingVariants-class	VariantType-class
CollapsedVCF	VCF-class
CollapsedVCF-class	VCF-class
cols,PolyPhenDb-method	PolyPhenDb-class
cols,SIFTDb-method	SIFTDb-class
contig	VCFHeader-class
contig,VCFHeader-method	VCFHeader-class
downstream	VariantType-class
downstream,AllVariants-method	VariantType-class
downstream,PromoterVariants-method	VariantType-class
downstream<-	VariantType-class
downstream<-,AllVariants-method	VariantType-class
downstream<-,PromoterVariants-method	VariantType-class
duplicateRSID	PolyPhenDb-class
expand,CollapsedVCF-method	VCF-class
expand,ExpandedVCF-method	VCF-class
ExpandedVCF	VCF-class
ExpandedVCF-class	VCF-class
filt	VCF-class
filt,VCF-method	VCF-class
filt<-	VCF-class
filt<-,VCF,character-method	VCF-class
filterVcf	filterVcf-methods
filterVcf,character-method	filterVcf-methods
filterVcf,TabixFile-method	filterVcf-methods
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,ANY-method	VCF-class
geno,VCF,character-method	VCF-class
geno,VCF,numeric-method	VCF-class
geno,VCF-method	VCF-class
geno,VCFHeader,ANY-method	VCF-class
geno,VCFHeader-method	VCFHeader-class
geno<-	VCF-class
geno<-,VCF,character,matrix-method	VCF-class
geno<-,VCF,missing,matrix-method	VCF-class
geno<-,VCF,missing,SimpleList-method	VCF-class
geno<-,VCF,numeric,matrix-method	VCF-class
genome,VCF-method	VCF-class
genotypeToSnpMatrix	genotypeToSnpMatrix-methods
genotypeToSnpMatrix,array-method	genotypeToSnpMatrix-methods
genotypeToSnpMatrix,CollapsedVCF-method	genotypeToSnpMatrix-methods
getTranscriptSeqs	getTranscriptSeqs-methods
getTranscriptSeqs,GRanges,FaFile-method	getTranscriptSeqs-methods
getTranscriptSeqs,GRangesList,BSgenome-method	getTranscriptSeqs-methods
getTranscriptSeqs,GRangesList,FaFile-method	getTranscriptSeqs-methods
GLtoGP	GLtoGP
header	VCFHeader-class
header,VCF-method	VCF-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-methods
locateVariants,GRanges,GRangesList,AllVariants-method	locateVariants-methods
locateVariants,GRanges,GRangesList,CodingVariants-method	locateVariants-methods
locateVariants,GRanges,GRangesList,FiveUTRVariants-method	locateVariants-methods
locateVariants,GRanges,GRangesList,IntergenicVariants-method	locateVariants-methods
locateVariants,GRanges,GRangesList,IntronVariants-method	locateVariants-methods
locateVariants,GRanges,GRangesList,PromoterVariants-method	locateVariants-methods
locateVariants,GRanges,GRangesList,SpliceSiteVariants-method	locateVariants-methods
locateVariants,GRanges,GRangesList,ThreeUTRVariants-method	locateVariants-methods
locateVariants,GRanges,GRangesList,VariantType-method	locateVariants-methods
locateVariants,GRanges,TranscriptDb,AllVariants-method	locateVariants-methods
locateVariants,GRanges,TranscriptDb,CodingVariants-method	locateVariants-methods
locateVariants,GRanges,TranscriptDb,FiveUTRVariants-method	locateVariants-methods
locateVariants,GRanges,TranscriptDb,IntergenicVariants-method	locateVariants-methods
locateVariants,GRanges,TranscriptDb,IntronVariants-method	locateVariants-methods
locateVariants,GRanges,TranscriptDb,PromoterVariants-method	locateVariants-methods
locateVariants,GRanges,TranscriptDb,SpliceSiteVariants-method	locateVariants-methods
locateVariants,GRanges,TranscriptDb,ThreeUTRVariants-method	locateVariants-methods
locateVariants,GRanges,TranscriptDb,VariantType-method	locateVariants-methods
locateVariants,Ranges,GRangesList,VariantType-method	locateVariants-methods
locateVariants,Ranges,TranscriptDb,VariantType-method	locateVariants-methods
locateVariants,VCF,GRangesList,VariantType-method	locateVariants-methods
locateVariants,VCF,TranscriptDb,VariantType-method	locateVariants-methods
MatrixToSnpMatrix	MatrixToSnpMatrix-methods
MatrixToSnpMatrix,matrix,DNAStringSet,DNAStringSetList-method	MatrixToSnpMatrix-methods
MatrixToSnpMatrix-deprecated	MatrixToSnpMatrix-methods
mcols<-,VCF-method	VCF-class
meta	VCFHeader-class
meta,VCFHeader-method	VCFHeader-class
metadata,PolyPhenDb-method	PolyPhenDb-class
metadata,SIFTDb-method	SIFTDb-class
PolyPhen	PolyPhenDb-class
PolyPhenDb	PolyPhenDb-class
PolyPhenDb-class	PolyPhenDb-class
PolyPhenDbColumns	PolyPhenDbColumns
predictCoding	predictCoding-methods
predictCoding,CollapsedVCF,TranscriptDb,ANY,missing-method	predictCoding-methods
predictCoding,ExpandedVCF,TranscriptDb,ANY,missing-method	predictCoding-methods
predictCoding,GRanges,TranscriptDb,ANY,DNAStringSet-method	predictCoding-methods
predictCoding,Ranges,TranscriptDb,ANY,DNAStringSet-method	predictCoding-methods
probabilityToSnpMatrix	probabilityToSnpMatrix
PromoterVariants	VariantType-class
PromoterVariants-class	VariantType-class
qual	VCF-class
qual,VCF-method	VCF-class
qual<-	VCF-class
qual<-,VCF,integer-method	VCF-class
rbind,VCF-method	VCF-class
readVcf	readVcf-methods
readVcf,character,character,missing-method	readVcf-methods
readVcf,character,character,ScanVcfParam-method	readVcf-methods
readVcf,character,missing,missing-method	readVcf-methods
readVcf,TabixFile,character,GRanges-method	readVcf-methods
readVcf,TabixFile,character,GRangesList-method	readVcf-methods
readVcf,TabixFile,character,missing-method	readVcf-methods
readVcf,TabixFile,character,RangedData-method	readVcf-methods
readVcf,TabixFile,character,RangesList-method	readVcf-methods
readVcf,TabixFile,character,ScanVcfParam-method	readVcf-methods
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-methods
refLocsToLocalLocs,GRanges,missing,GRangesList-method	refLocsToLocalLocs-methods
refLocsToLocalLocs,GRanges,TranscriptDb,missing-method	refLocsToLocalLocs-methods
renameSeqlevels,VCF,character-method	VCF-class
rowData,VCF-method	VCF-class
rowData<-,VCF-method	VCF-class
samples	VCFHeader-class
samples,VCFHeader-method	VCFHeader-class
scanVcf	scanVcf-methods
scanVcf,character,missing-method	scanVcf-methods
scanVcf,character,ScanVcfParam-method	scanVcf-methods
scanVcf,connection,missing-method	scanVcf-methods
scanVcf,TabixFile,GRanges-method	scanVcf-methods
scanVcf,TabixFile,missing-method	scanVcf-methods
scanVcf,TabixFile,RangedData-method	scanVcf-methods
scanVcf,TabixFile,RangesList-method	scanVcf-methods
scanVcf,TabixFile,ScanVcfParam-method	scanVcf-methods
scanVcfHeader	scanVcf-methods
scanVcfHeader,character-method	scanVcf-methods
scanVcfHeader,TabixFile-method	scanVcf-methods
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,AllVariants-method	VariantType-class
show,CollapsedVCF-method	VCF-class
show,ExpandedVCF-method	VCF-class
show,PromoterVariants-method	VariantType-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
snpSummary	snpSummary
snpSummary,CollapsedVCF-method	snpSummary
SpliceSiteVariants	VariantType-class
SpliceSiteVariants-class	VariantType-class
strand,VCF-method	VCF-class
strand<-,VCF-method	VCF-class
summarizeVariants	summarizeVariants-methods
summarizeVariants,GRangesList,VCF,function-method	summarizeVariants-methods
summarizeVariants,GRangesList,VCF,VariantType-method	summarizeVariants-methods
summarizeVariants,TranscriptDb,VCF,CodingVariants-method	summarizeVariants-methods
summarizeVariants,TranscriptDb,VCF,FiveUTRVariants-method	summarizeVariants-methods
summarizeVariants,TranscriptDb,VCF,IntronVariants-method	summarizeVariants-methods
summarizeVariants,TranscriptDb,VCF,PromoterVariants-method	summarizeVariants-methods
summarizeVariants,TranscriptDb,VCF,SpliceSiteVariants-method	summarizeVariants-methods
summarizeVariants,TranscriptDb,VCF,ThreeUTRVariants-method	summarizeVariants-methods
ThreeUTRVariants	VariantType-class
ThreeUTRVariants-class	VariantType-class
updateObject,VCF-method	VCF-class
upstream	VariantType-class
upstream,AllVariants-method	VariantType-class
upstream,PromoterVariants-method	VariantType-class
upstream<-	VariantType-class
upstream<-,AllVariants-method	VariantType-class
upstream<-,PromoterVariants-method	VariantType-class
VariantType-class	VariantType-class
VCF	VCF-class
VCF-class	VCF-class
vcfFixed	ScanVcfParam-class
vcfFixed<-	ScanVcfParam-class
vcfGeno	ScanVcfParam-class
vcfGeno<-	ScanVcfParam-class
VCFHeader	VCFHeader-class
VCFHeader-class	VCFHeader-class
vcfInfo	ScanVcfParam-class
vcfInfo<-	ScanVcfParam-class
vcfTrimEmpty	ScanVcfParam-class
vcfTrimEmpty<-	ScanVcfParam-class
vcfWhich	ScanVcfParam-class
vcfWhich<-	ScanVcfParam-class
writeVcf	writeVcf-methods
writeVcf,VCF,character-method	writeVcf-methods
writeVcf,VCF,connection-method	writeVcf-methods
[,VCF,ANY,ANY-method	VCF-class
[,VCF-method	VCF-class
[<-,VCF,ANY,ANY,VCF-method	VCF-class
