API for VariantAnnotation
Annotation of Genetic Variants

Global functions
.HWEzscore	Source code
.baseSE	Source code
.checkArgs	Source code
.checkFile	Source code
.chunkIndex	Source code
.collapseLists	Source code
.consolidateHits	Source code
.contigsFromSeqinfo	Source code
.createAAColumn	Source code
.createMap	Source code
.createPPDbQuery	Source code
.createPROVEANDbQuery	Source code
.createSIFTDbQuery	Source code
.dispatchSNV_CollapsedVCF	Source code
.dispatchSNV_ExpandedVCF	Source code
.emptySnpMatrix	Source code
.emptySnpSummary	Source code
.expandAD	Source code
.expandGeno	Source code
.expandInfo	Source code
.filter	Source code
.formatALT	Source code
.formatHeader	Source code
.formatInfo	Source code
.formatList	Source code
.formatPPDbSelect	Source code
.formatPROVEANDbSelect	Source code
.formatRSID	Source code
.formatSIFTDbSelect	Source code
.geno2geno	Source code
.genotypeToIntegerSNV	Source code
.getKcol	Source code
.getRefCodons	Source code
.intergenic	Source code
.isDeletion	Source code
.isDelins	Source code
.isIndel	Source code
.isInsertion	Source code
.isSNV	Source code
.isStructural	Source code
.isSubstitution	Source code
.isTransition	Source code
.listMatrixToArray	Source code
.localCoordinates	Source code
.location	Source code
.makeResult	Source code
.makeVcfGeno	Source code
.makeVcfHeader	Source code
.makeVcfInfo	Source code
.makeVcfMatrix	Source code
.matrixOfListsToArray	Source code
.missingCols	Source code
.missingKeys	Source code
.pasteCollapseRows	Source code
.pasteMultiFieldDF	Source code
.predictCoding	Source code
.predictCodingGRangesList	Source code
.prefilter	Source code
.readLite	Source code
.readVcf	Source code
.recycleVector	Source code
.renameSamples	Source code
.returnEmpty	Source code
.rleRecycleVector	Source code
.scanVcfToVCF	Source code
.shiftRangeUpDown	Source code
.showHardFilters	Source code
.showVCFSubclass	Source code
.spliceSites	Source code
.sqlIn	Source code
.test	Source code
.testForSNV	Source code
.toDNAStringSetList	Source code
.unlistAltInfo	Source code
.unlistScan	Source code
.valid.ScanVcfParam	Source code
.valid.VCF	Source code
.valid.VCF.alt	Source code
.valid.VCF.fixed	Source code
.valid.VCF.info	Source code
.valid.VCFHeader	Source code
.valid.VCFHeader.colnames	Source code
.valid.VCFHeader.geno	Source code
.valid.VCFHeader.info	Source code
.valid.VCFHeader.meta	Source code
.valid.VCFHeadervsVCF	Source code
.valid.VCFHeadervsVCF.fields	Source code
.valid.VRanges	Source code
.valid.VRanges.depth	Source code
.valid.VRanges.ref	Source code
.valid.VRanges.strand	Source code
.vcf_map	Source code
.vcf_map_fixed	Source code
.vcf_map_samples	Source code
.vcf_scan	Source code
.vcf_scan_character	Source code
.vcf_scan_connection	Source code
.vcf_scan_header_maps	Source code
.vcf_usertag	Source code
AllVariants	Man page Source code
AllVariants-class	Man page
CodingVariants	Man page Source code
CodingVariants-class	Man page
CollapsedVCF	Man page
CollapsedVCF-class	Man page
CompressedVRangesList-class	Man page
ExpandedVCF	Man page
ExpandedVCF-class	Man page
FiveUTRVariants	Man page Source code
FiveUTRVariants-class	Man page
GLtoGP	Man page Source code
IntergenicVariants	Man page Source code
IntergenicVariants-class	Man page
IntronVariants	Man page Source code
IntronVariants-class	Man page
MatrixToSnpMatrix	Man page
PLtoGP	Man page Source code
PROVEAN	Man page
PROVEANDb	Man page
PROVEANDb-class	Man page
PolyPhen	Man page
PolyPhenDb	Man page
PolyPhenDb-class	Man page
PolyPhenDbColumns	Man page
PromoterVariants	Man page Source code
PromoterVariants-class	Man page
SIFT	Man page
SIFTDb	Man page
SIFTDb-class	Man page
SIFTDbColumns	Man page
ScanVcfParam	Man page
ScanVcfParam,ANY-method	Man page
ScanVcfParam,missing-method	Man page
ScanVcfParam-class	Man page
SimpleVRangesList-class	Man page
SnpMatrixToVCF	Man page Source code
SpliceSiteVariants	Man page Source code
SpliceSiteVariants-class	Man page
ThreeUTRVariants	Man page Source code
ThreeUTRVariants-class	Man page
UTRVariants	Source code
VCF	Man page Source code
VCF-class	Man page
VCFHeader	Man page Source code
VCFHeader-class	Man page
VRanges	Man page Man page Source code
VRanges-class	Man page
VRangesForMatching	Source code
VRangesList	Man page Source code
VRangesList-class	Man page
VRangesScanVcfParam	Man page Source code
VariantAnnotation-defunct	Man page
VariantType-class	Man page
VcfFile	Man page Source code
VcfFile-class	Man page
VcfFileList	Man page Source code
VcfFileList-class	Man page
[,VCF,ANY,ANY,ANY-method	Man page
[,VCF,ANY,ANY-method	Man page
[,VCF-method	Man page
[<-,VCF,ANY,ANY,VCF-method	Man page
`altDepth<-`	Source code
`refDepth<-`	Source code
`totalDepth<-`	Source code
addTotalDepthRuns	Source code
alt	Man page
alt,VCF-method	Man page
alt,VRanges-method	Man page
alt,VRangesList-method	Man page
alt<-	Man page
alt<-,CollapsedVCF,CharacterList-method	Man page
alt<-,CollapsedVCF,DNAStringSetList-method	Man page
alt<-,ExpandedVCF,DNAStringSet-method	Man page
alt<-,ExpandedVCF,character-method	Man page
alt<-,VRanges,ANY-method	Man page
altDepth	Man page
altDepth,VRanges-method	Man page
altDepth<-	Man page
altDepth<-,VRanges-method	Man page
altFraction	Man page
altFraction,VRanges-method	Man page
asVCF	Man page
asVCF,VRanges-method	Man page
called	Man page
called,VRanges-method	Man page
cbind,VCF-method	Man page
characterOrRle-class	Man page
characterRle-class	Man page
class:CollapsedVCF	Man page
class:CompressedVRangesList	Man page
class:ExpandedVCF	Man page
class:PROVEANDb	Man page
class:PolyPhenDb	Man page
class:SIFTDb	Man page
class:SimpleVRangesList	Man page
class:VCF	Man page
class:VRanges	Man page
class:VRangesList	Man page
coerce,GRanges,VRanges-method	Man page
coerce,VCF,VRanges-method	Man page
coerce,VRanges,VCF-method	Man page
columns,PROVEANDb-method	Man page
columns,PolyPhenDb-method	Man page
columns,SIFTDb-method	Man page
complexRle-class	Man page
contig	Man page
contig,VCFHeader-method	Man page
dbSNPFilter	Man page
dimnames<-,VCF,list-method	Man page
downstream	Man page
downstream,AllVariants-method	Man page
downstream,IntergenicVariants-method	Man page
downstream,PromoterVariants-method	Man page
downstream<-	Man page
downstream<-,AllVariants-method	Man page
downstream<-,IntergenicVariants-method	Man page
downstream<-,PromoterVariants-method	Man page
duplicateRSID	Man page Source code
expand,CollapsedVCF-method	Man page
expand,ExpandedVCF-method	Man page
factorOrRle-class	Man page
factorRle-class	Man page
filt	Man page
filt,VCF-method	Man page
filt<-	Man page
filt<-,VCF,character-method	Man page
filterVcf	Man page
filterVcf,TabixFile-method	Man page
filterVcf,character-method	Man page
fixed	Man page
fixed,VCF-method	Man page
fixed,VCFHeader-method	Man page
fixed<-	Man page
fixed<-,VCF,DataFrame-method	Man page
fixed<-,VCFHeader,DataFrameList-method	Man page
gVCFRunEnds	Source code
geno	Man page
geno,VCF,ANY-method	Man page
geno,VCF,character-method	Man page
geno,VCF,numeric-method	Man page
geno,VCF-method	Man page
geno,VCFHeader,ANY-method	Man page
geno,VCFHeader-method	Man page
geno<-	Man page
geno<-,VCF,character,matrix-method	Man page
geno<-,VCF,missing,SimpleList-method	Man page
geno<-,VCF,missing,matrix-method	Man page
geno<-,VCF,numeric,matrix-method	Man page
geno<-,VCFHeader,missing,DataFrame-method	Man page
genoToMCol	Source code
genome,VCF-method	Man page
genotypeCodesToNucleotides	Man page Source code
genotypeToSnpMatrix	Man page
genotypeToSnpMatrix,CollapsedVCF-method	Man page
genotypeToSnpMatrix,array-method	Man page
getTranscriptSeqs	Man page
getTranscriptSeqs,GRanges,FaFile-method	Man page
getTranscriptSeqs,GRangesList,ANY-method	Man page
getTranscriptSeqs,GRangesList,BSgenome-method	Man page
getTranscriptSeqs,GRangesList,FaFile-method	Man page
hardFilters	Man page
hardFilters,VRanges-method	Man page
hardFilters<-	Man page
hardFilters<-,VRanges-method	Man page
header	Man page
header,VCF-method	Man page
header,VCFHeader-method	Man page
header<-	Man page
header<-,VCF,VCFHeader-method	Man page
idType	Man page
idType,IntergenicVariants-method	Man page
idType<-	Man page
idType<-,IntergenicVariants-method	Man page
import,VcfFile,ANY,ANY-method	Man page
indexVcf	Man page
indexVcf,VcfFile-method	Man page
indexVcf,VcfFileList-method	Man page
indexVcf,character-method	Man page
info	Man page
info,VCF-method	Man page
info,VCFHeader-method	Man page
info<-	Man page
info<-,VCF,DataFrame-method	Man page
info<-,VCFHeader,DataFrame-method	Man page
integerOrRle-class	Man page
integerRle-class	Man page
intergenic	Man page
intergenic,AllVariants-method	Man page
intergenic<-	Man page
intergenic<-,AllVariants-method	Man page
isDeletion	Man page
isDeletion,CollapsedVCF-method	Man page
isDeletion,ExpandedVCF-method	Man page
isDeletion,VRanges-method	Man page
isDelins	Man page
isDelins,CollapsedVCF-method	Man page
isDelins,ExpandedVCF-method	Man page
isDelins,VRanges-method	Man page
isGVCFRun	Source code
isIndel	Man page
isIndel,CollapsedVCF-method	Man page
isIndel,ExpandedVCF-method	Man page
isIndel,VRanges-method	Man page
isInsertion	Man page
isInsertion,CollapsedVCF-method	Man page
isInsertion,ExpandedVCF-method	Man page
isInsertion,VRanges-method	Man page
isSNV	Man page
isSNV,CollapsedVCF-method	Man page
isSNV,ExpandedVCF-method	Man page
isSNV,VRanges-method	Man page
isSubstitution	Man page
isSubstitution,CollapsedVCF-method	Man page
isSubstitution,ExpandedVCF-method	Man page
isSubstitution,VRanges-method	Man page
isTransition	Man page
isTransition,CollapsedVCF-method	Man page
isTransition,ExpandedVCF-method	Man page
isTransition,VRanges-method	Man page
keys,PROVEANDb-method	Man page
keys,PolyPhenDb-method	Man page
keys,SIFTDb-method	Man page
keytypes,PROVEANDb-method	Man page
locateVariants	Man page
locateVariants,GRanges,GRangesList,AllVariants-method	Man page
locateVariants,GRanges,GRangesList,CodingVariants-method	Man page
locateVariants,GRanges,GRangesList,FiveUTRVariants-method	Man page
locateVariants,GRanges,GRangesList,IntergenicVariants-method	Man page
locateVariants,GRanges,GRangesList,IntronVariants-method	Man page
locateVariants,GRanges,GRangesList,PromoterVariants-method	Man page
locateVariants,GRanges,GRangesList,SpliceSiteVariants-method	Man page
locateVariants,GRanges,GRangesList,ThreeUTRVariants-method	Man page
locateVariants,GRanges,GRangesList,VariantType-method	Man page
locateVariants,GRanges,TxDb,AllVariants-method	Man page
locateVariants,GRanges,TxDb,CodingVariants-method	Man page
locateVariants,GRanges,TxDb,FiveUTRVariants-method	Man page
locateVariants,GRanges,TxDb,IntergenicVariants-method	Man page
locateVariants,GRanges,TxDb,IntronVariants-method	Man page
locateVariants,GRanges,TxDb,PromoterVariants-method	Man page
locateVariants,GRanges,TxDb,SpliceSiteVariants-method	Man page
locateVariants,GRanges,TxDb,ThreeUTRVariants-method	Man page
locateVariants,GRanges,TxDb,VariantType-method	Man page
locateVariants,IntegerRanges,GRangesList,VariantType-method	Man page
locateVariants,IntegerRanges,TxDb,VariantType-method	Man page
locateVariants,VCF,GRangesList,VariantType-method	Man page
locateVariants,VCF,TxDb,VariantType-method	Man page
logicalRle-class	Man page
makeFILTERheader	Source code
makeFILTERstrings	Source code
makeFORMATheader	Source code
makeINFOheader	Source code
makeVRangesFromGRanges	Man page Source code
match,VRanges,VRanges-method	Man page
mcols<-,VCF,ANY-method	Man page
mcols<-,VCF-method	Man page
meta	Man page
meta,VCFHeader-method	Man page
meta<-	Man page
meta<-,VCFHeader,DataFrame-method	Man page
meta<-,VCFHeader,DataFrameList-method	Man page
metadata,PolyPhenDb-method	Man page
metadata,SIFTDb-method	Man page
naToZero	Source code
numericRle-class	Man page
parseFilterStrings	Source code
pileupGRanges	Source code
predictCoding	Man page
predictCoding,CollapsedVCF,TxDb,ANY,missing-method	Man page
predictCoding,ExpandedVCF,TxDb,ANY,missing-method	Man page
predictCoding,GRanges,TxDb,ANY,DNAStringSet-method	Man page
predictCoding,IntegerRanges,TxDb,ANY,DNAStringSet-method	Man page
predictCoding,VRanges,TxDb,ANY,missing-method	Man page
probabilityToSnpMatrix	Man page Source code
promoter	Man page
promoter,AllVariants-method	Man page
promoter<-	Man page
promoter<-,AllVariants-method	Man page
qual	Man page
qual,VCF-method	Man page
qual<-	Man page
qual<-,VCF,numeric-method	Man page
rawRle-class	Man page
rbind,VCF-method	Man page
readGT	Man page Source code
readGeno	Man page Source code
readInfo	Man page Source code
readVcf	Man page
readVcf,TabixFile,GRanges-method	Man page
readVcf,TabixFile,GRangesList-method	Man page
readVcf,TabixFile,IntegerRangesList-method	Man page
readVcf,TabixFile,ScanVcfParam-method	Man page
readVcf,TabixFile,missing-method	Man page
readVcf,character,ANY-method	Man page
readVcf,character,missing-method	Man page Man page
readVcfAsVRanges	Man page Source code
readVcfLongForm	Man page
readVcfLongForm,TabixFile,character,GRanges-method	Man page
readVcfLongForm,TabixFile,character,IntegerRangesList-method	Man page
readVcfLongForm,TabixFile,character,ScanVcfParam-method	Man page
readVcfLongForm,TabixFile,character,missing-method	Man page
readVcfLongForm,character,character,ScanVcfParam-method	Man page
readVcfLongForm,character,character,missing-method	Man page
readVcfLongForm,character,missing,missing-method	Man page
ref	Man page
ref,VCF-method	Man page
ref,VRanges-method	Man page
ref,VRangesList-method	Man page
ref<-	Man page
ref<-,VCF,DNAStringSet-method	Man page
ref<-,VRanges,ANY-method	Man page
refDepth	Man page
refDepth,VRanges-method	Man page
refDepth<-	Man page
refDepth<-,VRanges-method	Man page
refLocsToLocalLocs	Man page
refLocsToLocalLocs,GRanges,TxDb,missing-method	Man page
refLocsToLocalLocs,GRanges,missing,GRangesList-method	Man page
reference	Man page
reference,VCFHeader-method	Man page
regionFilter	Man page
resetFilter	Man page Source code
restrictToSNV	Man page
rowRanges,VCF-method	Man page
rowRanges<-,VCF,GRanges-method	Man page
sampleNames,VRanges-method	Man page
sampleNames<-,VRanges,ANY-method	Man page
samples	Man page
samples,VCFHeader-method	Man page
scanVcf	Man page
scanVcf,TabixFile,GRanges-method	Man page
scanVcf,TabixFile,IntegerRangesList-method	Man page
scanVcf,TabixFile,ScanVcfParam-method	Man page
scanVcf,TabixFile,missing-method	Man page
scanVcf,character,ScanVcfParam-method	Man page
scanVcf,character,missing-method	Man page
scanVcf,connection,missing-method	Man page
scanVcfHeader	Man page
scanVcfHeader,TabixFile-method	Man page
scanVcfHeader,character-method	Man page
scanVcfHeader,missing-method	Man page
select,PROVEANDb-method	Man page
select,PolyPhenDb-method	Man page
select,SIFTDb-method	Man page
seqinfo	Man page
seqinfo,VCFHeader-method	Man page
seqinfo,VcfFile-method	Man page
seqinfo,VcfFileList-method	Man page
seqlevels,VCF-method	Man page
setAtomicRleUnion	Source code
setTypedRle	Source code
show,AllVariants-method	Man page
show,CollapsedVCF-method	Man page
show,ExpandedVCF-method	Man page
show,PromoterVariants-method	Man page
show,VCF-method	Man page
show,VCFHeader-method	Man page
show,VariantType-method	Man page
snpSummary	Man page
snpSummary,CollapsedVCF-method	Man page
softFilter	Man page Source code
softFilterMatrix	Man page
softFilterMatrix,VRanges-method	Man page
softFilterMatrix<-	Man page
softFilterMatrix<-,VRanges-method	Man page
stackSamples	Man page
stackSamples,VRangesList-method	Man page
strand,VCF-method	Man page
strand<-,VCF,ANY-method	Man page
subset,VCF-method	Man page
summarizeVariants	Man page
summarizeVariants,GRangesList,VCF,VariantType-method	Man page
summarizeVariants,GRangesList,VCF,function-method	Man page
summarizeVariants,TxDb,VCF,CodingVariants-method	Man page
summarizeVariants,TxDb,VCF,FiveUTRVariants-method	Man page
summarizeVariants,TxDb,VCF,IntronVariants-method	Man page
summarizeVariants,TxDb,VCF,PromoterVariants-method	Man page
summarizeVariants,TxDb,VCF,SpliceSiteVariants-method	Man page
summarizeVariants,TxDb,VCF,ThreeUTRVariants-method	Man page
tabulate	Man page
tabulate,VRanges-method	Man page
totalDepth	Man page
totalDepth,VRanges-method	Man page
totalDepth<-	Man page
totalDepth<-,VRanges-method	Man page
upstream	Man page
upstream,AllVariants-method	Man page
upstream,IntergenicVariants-method	Man page
upstream,PromoterVariants-method	Man page
upstream<-	Man page
upstream<-,AllVariants-method	Man page
upstream<-,IntergenicVariants-method	Man page
upstream<-,PromoterVariants-method	Man page
vcfFields	Man page
vcfFields,VCF-method	Man page
vcfFields,VCFHeader-method	Man page
vcfFields,VcfFile-method	Man page
vcfFields,VcfFileList-method	Man page
vcfFields,character-method	Man page
vcfFields,missing-method	Man page
vcfFixed	Man page Source code
vcfFixed<-	Man page
vcfGeno	Man page Source code
vcfGeno<-	Man page
vcfInfo	Man page Source code
vcfInfo<-	Man page
vcfSamples	Man page Source code
vcfSamples<-	Man page
vcfTrimEmpty	Man page Source code
vcfTrimEmpty<-	Man page
vcfWhich	Man page Source code
vcfWhich<-	Man page
vranges2Vcf	Source code
writeVcf	Man page
writeVcf,VCF,character-method	Man page
writeVcf,VCF,connection-method	Man page
writeVcf,VRanges,ANY-method	Man page