AllVariants	VariantType-class
AllVariants-class	VariantType-class
alt	VCF-class
alt,VCF-method	VCF-class
alt,VRanges-method	VRanges-class
alt,VRangesList-method	VRangesList-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
alt<-,VRanges,ANY-method	VRanges-class
altDepth	VRanges-class
altDepth,VRanges-method	VRanges-class
altDepth<-	VRanges-class
altDepth<-,VRanges-method	VRanges-class
altFraction	VRanges-class
altFraction,VRanges-method	VRanges-class
asVCF	VRanges-class
asVCF,VRanges-method	VRanges-class
called	VRanges-class
called,VRanges-method	VRanges-class
cbind,VCF-method	VCF-class
characterOrRle-class	VRanges-class
characterRle-class	VRanges-class
class:CollapsedVCF	VCF-class
class:CompressedVRangesList	VRangesList-class
class:ExpandedVCF	VCF-class
class:PolyPhenDb	PolyPhenDb-class
class:PROVEANDb	PROVEANDb-class
class:SIFTDb	SIFTDb-class
class:SimpleVRangesList	VRangesList-class
class:VCF	VCF-class
class:VRanges	VRanges-class
class:VRangesList	VRangesList-class
CodingVariants	VariantType-class
CodingVariants-class	VariantType-class
coerce,GRanges,VRanges-method	VRanges-class
coerce,VCF,VRanges-method	VRanges-class
coerce,VRanges,VCF-method	VRanges-class
CollapsedVCF	VCF-class
CollapsedVCF-class	VCF-class
columns,PolyPhenDb-method	PolyPhenDb-class
columns,PROVEANDb-method	PROVEANDb-class
columns,SIFTDb-method	SIFTDb-class
complexRle-class	VRanges-class
CompressedVRangesList-class	VRangesList-class
contig	VCFHeader-class
contig,VCFHeader-method	VCFHeader-class
dbSNPFilter	defunct
dimnames<-,VCF,list-method	VCF-class
downstream	VariantType-class
downstream,AllVariants-method	VariantType-class
downstream,IntergenicVariants-method	VariantType-class
downstream,PromoterVariants-method	VariantType-class
downstream<-	VariantType-class
downstream<-,AllVariants-method	VariantType-class
downstream<-,IntergenicVariants-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
factorOrRle-class	VRanges-class
factorRle-class	VRanges-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
fixed<-,VCFHeader,DataFrameList-method	VCFHeader-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
geno<-,VCFHeader,missing,DataFrame-method	VCFHeader-class
genome,VCF-method	VCF-class
genotypeCodesToNucleotides	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,ANY-method	getTranscriptSeqs-methods
getTranscriptSeqs,GRangesList,BSgenome-method	getTranscriptSeqs-methods
getTranscriptSeqs,GRangesList,FaFile-method	getTranscriptSeqs-methods
GLtoGP	GLtoGP
hardFilters	VRanges-class
hardFilters,VRanges-method	VRanges-class
hardFilters<-	VRanges-class
hardFilters<-,VRanges-method	VRanges-class
header	VCFHeader-class
header,VCF-method	VCF-class
header,VCFHeader-method	VCFHeader-class
header<-	VCF-class
header<-,VCF,VCFHeader-method	VCF-class
idType	VariantType-class
idType,IntergenicVariants-method	VariantType-class
idType<-	VariantType-class
idType<-,IntergenicVariants-method	VariantType-class
import,VcfFile,ANY,ANY-method	readVcf-methods
indexVcf	indexVcf-method
indexVcf,character-method	indexVcf-method
indexVcf,VcfFile-method	indexVcf-method
indexVcf,VcfFileList-method	indexVcf-method
info	VCF-class
info,VCF-method	VCF-class
info,VCFHeader-method	VCFHeader-class
info<-	VCF-class
info<-,VCF,DataFrame-method	VCF-class
info<-,VCFHeader,DataFrame-method	VCFHeader-class
integerOrRle-class	VRanges-class
integerRle-class	VRanges-class
intergenic	VariantType-class
intergenic,AllVariants-method	VariantType-class
intergenic<-	VariantType-class
intergenic<-,AllVariants-method	VariantType-class
IntergenicVariants	VariantType-class
IntergenicVariants-class	VariantType-class
IntronVariants	VariantType-class
IntronVariants-class	VariantType-class
isDeletion	isSNV-methods
isDeletion,CollapsedVCF-method	isSNV-methods
isDeletion,ExpandedVCF-method	isSNV-methods
isDeletion,VRanges-method	isSNV-methods
isDelins	isSNV-methods
isDelins,CollapsedVCF-method	isSNV-methods
isDelins,ExpandedVCF-method	isSNV-methods
isDelins,VRanges-method	isSNV-methods
isIndel	isSNV-methods
isIndel,CollapsedVCF-method	isSNV-methods
isIndel,ExpandedVCF-method	isSNV-methods
isIndel,VRanges-method	isSNV-methods
isInsertion	isSNV-methods
isInsertion,CollapsedVCF-method	isSNV-methods
isInsertion,ExpandedVCF-method	isSNV-methods
isInsertion,VRanges-method	isSNV-methods
isSNV	isSNV-methods
isSNV,CollapsedVCF-method	isSNV-methods
isSNV,ExpandedVCF-method	isSNV-methods
isSNV,VRanges-method	isSNV-methods
isSubstitution	isSNV-methods
isSubstitution,CollapsedVCF-method	isSNV-methods
isSubstitution,ExpandedVCF-method	isSNV-methods
isSubstitution,VRanges-method	isSNV-methods
isTransition	isSNV-methods
isTransition,CollapsedVCF-method	isSNV-methods
isTransition,ExpandedVCF-method	isSNV-methods
isTransition,VRanges-method	isSNV-methods
keys,PolyPhenDb-method	PolyPhenDb-class
keys,PROVEANDb-method	PROVEANDb-class
keys,SIFTDb-method	SIFTDb-class
keytypes,PROVEANDb-method	PROVEANDb-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,TxDb,AllVariants-method	locateVariants-methods
locateVariants,GRanges,TxDb,CodingVariants-method	locateVariants-methods
locateVariants,GRanges,TxDb,FiveUTRVariants-method	locateVariants-methods
locateVariants,GRanges,TxDb,IntergenicVariants-method	locateVariants-methods
locateVariants,GRanges,TxDb,IntronVariants-method	locateVariants-methods
locateVariants,GRanges,TxDb,PromoterVariants-method	locateVariants-methods
locateVariants,GRanges,TxDb,SpliceSiteVariants-method	locateVariants-methods
locateVariants,GRanges,TxDb,ThreeUTRVariants-method	locateVariants-methods
locateVariants,GRanges,TxDb,VariantType-method	locateVariants-methods
locateVariants,IntegerRanges,GRangesList,VariantType-method	locateVariants-methods
locateVariants,IntegerRanges,TxDb,VariantType-method	locateVariants-methods
locateVariants,VCF,GRangesList,VariantType-method	locateVariants-methods
locateVariants,VCF,TxDb,VariantType-method	locateVariants-methods
logicalRle-class	VRanges-class
makeVRangesFromGRanges	VRanges-class
match,VRanges,VRanges-method	VRanges-class
MatrixToSnpMatrix	defunct
mcols<-,VCF,ANY-method	VCF-class
mcols<-,VCF-method	VCF-class
meta	VCFHeader-class
meta,VCFHeader-method	VCFHeader-class
meta<-	VCFHeader-class
meta<-,VCFHeader,DataFrame-method	VCFHeader-class
meta<-,VCFHeader,DataFrameList-method	VCFHeader-class
metadata,PolyPhenDb-method	PolyPhenDb-class
metadata,SIFTDb-method	SIFTDb-class
numericRle-class	VRanges-class
PLtoGP	GLtoGP
PolyPhen	PolyPhenDb-class
PolyPhenDb	PolyPhenDb-class
PolyPhenDb-class	PolyPhenDb-class
PolyPhenDbColumns	PolyPhenDbColumns
predictCoding	predictCoding-methods
predictCoding,CollapsedVCF,TxDb,ANY,missing-method	predictCoding-methods
predictCoding,ExpandedVCF,TxDb,ANY,missing-method	predictCoding-methods
predictCoding,GRanges,TxDb,ANY,DNAStringSet-method	predictCoding-methods
predictCoding,IntegerRanges,TxDb,ANY,DNAStringSet-method	predictCoding-methods
predictCoding,VRanges,TxDb,ANY,missing-method	predictCoding-methods
probabilityToSnpMatrix	probabilityToSnpMatrix
promoter	VariantType-class
promoter,AllVariants-method	VariantType-class
promoter<-	VariantType-class
promoter<-,AllVariants-method	VariantType-class
PromoterVariants	VariantType-class
PromoterVariants-class	VariantType-class
PROVEAN	PROVEANDb-class
PROVEANDb	PROVEANDb-class
PROVEANDb-class	PROVEANDb-class
qual	VCF-class
qual,VCF-method	VCF-class
qual<-	VCF-class
qual<-,VCF,numeric-method	VCF-class
rawRle-class	VRanges-class
rbind,VCF-method	VCF-class
readGeno	readVcf-methods
readGT	readVcf-methods
readInfo	readVcf-methods
readVcf	readVcf-methods
readVcf,character,ANY-method	readVcf-methods
readVcf,character,missing-method	readVcf-methods
readVcf,TabixFile,GRanges-method	readVcf-methods
readVcf,TabixFile,GRangesList-method	readVcf-methods
readVcf,TabixFile,IntegerRangesList-method	readVcf-methods
readVcf,TabixFile,missing-method	readVcf-methods
readVcf,TabixFile,ScanVcfParam-method	readVcf-methods
readVcfAsVRanges	VRanges-class
readVcfLongForm	defunct
readVcfLongForm,character,character,missing-method	defunct
readVcfLongForm,character,character,ScanVcfParam-method	defunct
readVcfLongForm,character,missing,missing-method	defunct
readVcfLongForm,TabixFile,character,GRanges-method	defunct
readVcfLongForm,TabixFile,character,IntegerRangesList-method	defunct
readVcfLongForm,TabixFile,character,missing-method	defunct
readVcfLongForm,TabixFile,character,ScanVcfParam-method	defunct
ref	VCF-class
ref,VCF-method	VCF-class
ref,VRanges-method	VRanges-class
ref,VRangesList-method	VRangesList-class
ref<-	VCF-class
ref<-,VCF,DNAStringSet-method	VCF-class
ref<-,VRanges,ANY-method	VRanges-class
refDepth	VRanges-class
refDepth,VRanges-method	VRanges-class
refDepth<-	VRanges-class
refDepth<-,VRanges-method	VRanges-class
reference	VCFHeader-class
reference,VCFHeader-method	VCFHeader-class
refLocsToLocalLocs	defunct
refLocsToLocalLocs,GRanges,missing,GRangesList-method	defunct
refLocsToLocalLocs,GRanges,TxDb,missing-method	defunct
regionFilter	defunct
resetFilter	VRanges-class
restrictToSNV	defunct
rowRanges,VCF-method	VCF-class
rowRanges<-,VCF,GRanges-method	VCF-class
sampleNames,VRanges-method	VRanges-class
sampleNames<-,VRanges,ANY-method	VRanges-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,IntegerRangesList-method	scanVcf-methods
scanVcf,TabixFile,missing-method	scanVcf-methods
scanVcf,TabixFile,ScanVcfParam-method	scanVcf-methods
scanVcfHeader	scanVcf-methods
scanVcfHeader,character-method	scanVcf-methods
scanVcfHeader,missing-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,PROVEANDb-method	PROVEANDb-class
select,SIFTDb-method	SIFTDb-class
seqinfo	seqinfo-method
seqinfo,VcfFile-method	seqinfo-method
seqinfo,VcfFileList-method	seqinfo-method
seqinfo,VCFHeader-method	VCFHeader-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
SimpleVRangesList-class	VRangesList-class
SnpMatrixToVCF	VCF-class
snpSummary	snpSummary
snpSummary,CollapsedVCF-method	snpSummary
softFilter	VRanges-class
softFilterMatrix	VRanges-class
softFilterMatrix,VRanges-method	VRanges-class
softFilterMatrix<-	VRanges-class
softFilterMatrix<-,VRanges-method	VRanges-class
SpliceSiteVariants	VariantType-class
SpliceSiteVariants-class	VariantType-class
stackSamples	VRangesList-class
stackSamples,VRangesList-method	VRangesList-class
strand,VCF-method	VCF-class
strand<-,VCF,ANY-method	VCF-class
subset,VCF-method	VCF-class
summarizeVariants	summarizeVariants-methods
summarizeVariants,GRangesList,VCF,function-method	summarizeVariants-methods
summarizeVariants,GRangesList,VCF,VariantType-method	summarizeVariants-methods
summarizeVariants,TxDb,VCF,CodingVariants-method	summarizeVariants-methods
summarizeVariants,TxDb,VCF,FiveUTRVariants-method	summarizeVariants-methods
summarizeVariants,TxDb,VCF,IntronVariants-method	summarizeVariants-methods
summarizeVariants,TxDb,VCF,PromoterVariants-method	summarizeVariants-methods
summarizeVariants,TxDb,VCF,SpliceSiteVariants-method	summarizeVariants-methods
summarizeVariants,TxDb,VCF,ThreeUTRVariants-method	summarizeVariants-methods
tabulate	VRanges-class
tabulate,VRanges-method	VRanges-class
ThreeUTRVariants	VariantType-class
ThreeUTRVariants-class	VariantType-class
totalDepth	VRanges-class
totalDepth,VRanges-method	VRanges-class
totalDepth<-	VRanges-class
totalDepth<-,VRanges-method	VRanges-class
updateObject,VCF-method	VCF-class
upstream	VariantType-class
upstream,AllVariants-method	VariantType-class
upstream,IntergenicVariants-method	VariantType-class
upstream,PromoterVariants-method	VariantType-class
upstream<-	VariantType-class
upstream<-,AllVariants-method	VariantType-class
upstream<-,IntergenicVariants-method	VariantType-class
upstream<-,PromoterVariants-method	VariantType-class
VariantAnnotation-defunct	defunct
VariantType-class	VariantType-class
VCF	VCF-class
VCF-class	VCF-class
vcfFields	VCFHeader-class
vcfFields,character-method	VcfFile-class
vcfFields,missing-method	VcfFile-class
vcfFields,VCF-method	VCF-class
vcfFields,VcfFile-method	VcfFile-class
vcfFields,VcfFileList-method	VcfFile-class
vcfFields,VCFHeader-method	VCFHeader-class
VcfFile	VcfFile-class
VcfFile-class	VcfFile-class
VcfFileList	VcfFile-class
VcfFileList-class	VcfFile-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
vcfSamples	ScanVcfParam-class
vcfSamples<-	ScanVcfParam-class
vcfTrimEmpty	ScanVcfParam-class
vcfTrimEmpty<-	ScanVcfParam-class
vcfWhich	ScanVcfParam-class
vcfWhich<-	ScanVcfParam-class
VRanges	VRanges-class
VRanges-class	VRanges-class
VRangesList	VRangesList-class
VRangesList-class	VRangesList-class
VRangesScanVcfParam	defunct
writeVcf	writeVcf-methods
writeVcf,VCF,character-method	writeVcf-methods
writeVcf,VCF,connection-method	writeVcf-methods
writeVcf,VRanges,ANY-method	VRanges-class
[,VCF,ANY,ANY,ANY-method	VCF-class
[,VCF,ANY,ANY-method	VCF-class
[,VCF-method	VCF-class
[<-,VCF,ANY,ANY,VCF-method	VCF-class
