API for vobencha/VariantAnnotation
Annotation of Genetic Variants

Global functions
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
HWEzscore 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
addTotalDepthRuns Source code
alt Man page
alt,VCF-method Man page
alt,VRanges-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
baseSE Source code
called Man page
called,VRanges-method Man page
cbind,VCF-method Man page
characterOrRle-class Man page
characterRle-class Man page
checkArgs Source code
checkFile Source code
checkLength Source code
chunkIndex Source code
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
collapseLists Source code
columns,PROVEANDb-method Man page
columns,PolyPhenDb-method Man page
columns,SIFTDb-method Man page
complexRle-class Man page
consolidateHits Source code
contig Man page
contig,VCFHeader-method Man page
contigsFromSeqinfo Source code
createAAColumn Source code
createMap Source code
createPPDbQuery Source code
createPROVEANDbQuery Source code
createSIFTDbQuery Source code
dbSNPFilter Man page
dimnames<-,VCF,list-method Man page
dispatchSNV_CollapsedVCF Source code
dispatchSNV_ExpandedVCF Source code
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
emptySnpMatrix Source code
emptySnpSummary Source code
expand,CollapsedVCF-method Man page
expand,ExpandedVCF-method Man page
expandAD Source code
expandGeno Source code
expandInfo Source code
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
filter Source code
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
formatALT Source code
formatHeader Source code
formatInfo Source code
formatList Source code
formatPPDbSelect Source code
formatPROVEANDbSelect Source code
formatRSID Source code
formatSIFTDbSelect Source code
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
geno2geno Source code
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
genotypeToIntegerSNV Source code
genotypeToSnpMatrix Man page
genotypeToSnpMatrix,CollapsedVCF-method Man page
genotypeToSnpMatrix,array-method Man page
getKcol Source code
getRefCodons Source code
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
listMatrixToArray Source code
localCoordinates Source code
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,Ranges,GRangesList,VariantType-method Man page
locateVariants,Ranges,TxDb,VariantType-method Man page
locateVariants,VCF,GRangesList,VariantType-method Man page
locateVariants,VCF,TxDb,VariantType-method Man page
location Source code
logicalRle-class Man page
makeFILTERheader Source code
makeFILTERstrings Source code
makeFORMATheader Source code
makeINFOheader Source code
makeResult Source code
makeVRangesFromGRanges Man page Source code
makeVcfGeno Source code
makeVcfHeader Source code
makeVcfInfo Source code
makeVcfMatrix Source code
match,VRanges,VRanges-method Man page
matrixOfListsToArray Source code
mcols<-,VCF,DataFrame-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
missingCols Source code
missingKeys Source code
naToZero Source code
ntergenic Source code
numericRle-class Man page
parseFilterStrings Source code
pasteCollapseRows Source code
pileupGRanges Source code
predictCoding Man page Source code
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,Ranges,TxDb,ANY,DNAStringSet-method Man page
predictCoding,VRanges,TxDb,ANY,missing-method Man page
predictCodingGRangesList Source code
prefilter Source code
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
readLite Source code
readVcf Man page Source code
readVcf,TabixFile,GRanges-method Man page
readVcf,TabixFile,GRangesList-method Man page
readVcf,TabixFile,RangesList-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,RangesList-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<- 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
renameSamples Source code
resetFilter Man page Source code
restrictToSNV Man page Source code
returnEmpty Source code
rleRecycleVector Source code
rowRanges,VCF-method Man page
rowRanges<-,VCF-method Man page
sDeletion Source code
sDelins Source code
sIndel Source code
sInsertion Source code
sSNV Source code
sStructural Source code
sSubstitution Source code
sTransition Source code
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,RangesList-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
scanVcfToVCF Source code
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
shiftRangeUpDown 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
showHardFilters Source code
showVCFSubclass Source code
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
spliceSites Source code
sqlIn Source code
stackSamples Man page
stackSamples,VRangesList-method Man page
strand,VCF-method Man page
strand<-,VCF,ANY-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
test Source code
testForSNV Source code
toDNAStringSetList Source code
totalDepth Man page
totalDepth,VRanges-method Man page
totalDepth<- Man page
totalDepth<-,VRanges-method Man page
unlistAltInfo Source code
unlistScan Source code
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
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
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
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
vranges2Vcf Source code
writeVcf Man page
writeVcf,VCF,character-method Man page
writeVcf,VCF,connection-method Man page
writeVcf,VRanges,ANY-method Man page
vobencha/VariantAnnotation documentation built on May 10, 2017, 6:09 a.m.