jmacdon/AnnotationDbi
Manipulation of SQLite-based annotations in Bioconductor

Package index
Search the jmacdon/AnnotationDbi package
Vignettes
Functions
696
Source code
49
Man pages
25
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jmacdon/AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor
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API

API for jmacdon/AnnotationDbi
Manipulation of SQLite-based annotations in Bioconductor

Global functions
$,Bimap-method Man page
.Bimap.summary Source code
.GOid2go_synonymField Source code
.GOid2go_termField Source code
.GetLKeyLength Source code
.GetUniqueLKeys Source code
.L2Rchain.toString Source code
.addRevMapSeeds Source code
.adjustForDupColNames Source code
.alignAnnList Source code
.appendGenesToTabs Source code
.attachDB Source code
.attachDBs Source code
.attachGO Source code
.attach_supporting_pkg Source code
.checkForDeprecatedKeytype Source code
.checkKeys Source code
.checkKeysAreWellFormed Source code
.chooseJoinType Source code
.cleanup Source code
.collateQueryResults Source code
.cols Source code
.contextualizeColnames Source code
.convertGOtoGO2ALL Source code
.dbUniqueMappedKeys.SQLresultname Source code
.dbUniqueVals.SQLresultname Source code
.definePossibleTables Source code
.defineTables Source code
.deprecatedColsMessage Source code
.deriveTableNameFromField Source code
.doubleBracketSub Source code
.dropUnwantedRows Source code
.exists Source code
.expandCols Source code
.extractData Source code
.extractWithSimpleQuery Source code
.filterDeprecatedKeytypes Source code
.filterSuffixes Source code
.fishQuery Source code
.formatList Source code
.from.colpos Source code
.fromCol Source code
.generateExtraRows Source code
.generateQuery Source code
.get Source code
.getCentralID Source code
.getChipDbFile Source code
.getDBLoc Source code
.getDBLocs Source code
.getDataTables Source code
.getMappingData Source code
.getMetaValue Source code
.getOrgPkg Source code
.getTable Source code
.getTables Source code
.getaltDBs Source code
.handleMultipleMatches Source code
.hasMultiProbes Source code
.hasSingleProbes Source code
.inslot.Lkeys Source code
.inslot.Rkeys Source code
.is.submap Source code
.isSingleString Source code
.justFirstUpper Source code
.key.summary Source code
.keyColMapper Source code
.keys Source code
.keysReact Source code
.kosherPkg Source code
.legacyCols Source code
.legacyKeys Source code
.legacySelect Source code
.listDeprecatedKeytypes Source code
.ls Source code
.make0rowDataFrame Source code
.makeSQL Source code
.makeSQLchunks Source code
.mangleDBName Source code
.noSchemaCols Source code
.noSchemaKeys Source code
.noSchemaSelect Source code
.normalize.direction Source code
.ontoKeys Source code
.queryForKeys Source code
.reLabel Source code
.replaceValues Source code
.resortColumns Source code
.revmapper Source code
.sample Source code
.select Source code
.selectOnto Source code
.selectReact Source code
.selectWarnReact Source code
.simplifyCols Source code
.straightQuery Source code
.tagCol Source code
.taxonomyId Source code
.test Source code
.testForValidCols Source code
.testForValidKeys Source code
.testGOFrame Source code
.testKEGGFrame Source code
.to.colpos Source code
.toCol Source code
.toListOfLists Source code
.toSQLStringSet Source code
.toSQLWhere Source code
.toggleFilter Source code
.valid.colnames Source code
.valid.metadata.table Source code
.valid.table.colnames Source code
.warnAboutManyToOneRelationships Source code
ACCNUM Man page
ALIAS Man page
ARACYC Man page
ARACYCENZYME Man page
AgiAnnDbMap Man page
AgiAnnDbMap-class Man page
AnnDbBimap Man page
AnnDbBimap-class Man page
AnnDbMap Man page
AnnDbMap-class Man page
AnnDbObj Man page
AnnDbObj-class Man page
AnnDbObj-objects Man page
AnnDbPkg-checker Man page
AnnObj Man page
AnnObj-class Man page
AnnotationDb Man page Source code
AnnotationDb-class Man page
Bimap Man page Man page
Bimap-class Man page
Bimap-direction Man page
Bimap-envirAPI Man page
Bimap-keys Man page
Bimap-toTable Man page
BimapFormatting Man page
CHR Man page
CHRLOC Man page
CHRLOCEND Man page
COMMON Man page
ChipDb-class Man page
DEFINITION Man page
DESCRIPTION Man page
Definition Man page
Definition,GOTerms-method Man page
Definition,GOTermsAnnDbBimap-method Man page
Definition,character-method Man page
ENSEMBL Man page
ENSEMBLPROT Man page
ENSEMBLTRANS Man page
ENTREZID Man page
ENZYME Man page
EVIDENCE Man page
EVIDENCEALL Man page
FlatBimap Man page
FlatBimap-class Man page
GENENAME Man page
GO Man page
GOALL Man page
GOAllFrame Man page Man page
GOAllFrame,GOFrame-method Man page
GOAllFrame-class Man page
GODb-class Man page
GOFrame Man page Man page
GOFrame,data.frame,character-method Man page
GOFrame,data.frame,missing-method Man page
GOFrame-class Man page
GOID Man page Man page
GOID,GOTerms-method Man page
GOID,GOTermsAnnDbBimap-method Man page
GOID,character-method Man page
GOTerms Man page Source code
GOTerms-class Man page
GOTermsAnnDbBimap Man page
GOTermsAnnDbBimap-class Man page
Go3AnnDbBimap Man page
Go3AnnDbBimap-class Man page
Go3tablenames Source code
GoAnnDbBimap Man page
GoAnnDbBimap-class Man page
INTERPRO Man page
IPI Man page
InparanoidDb-class Man page
IpiAnnDbMap Man page
IpiAnnDbMap-class Man page
KEGGFrame Man page Man page
KEGGFrame,data.frame,character-method Man page
KEGGFrame,data.frame,missing-method Man page
KEGGFrame-class Man page
L2Rchain.Lfilter Source code
L2Rchain.Lkeyname Source code
L2Rchain.Ltablename Source code
L2Rchain.Rattribnames Source code
L2Rchain.Rfilter Source code
L2Rchain.Rkeyname Source code
L2Rchain.Rtablename Source code
L2Rchain.colmetanames Source code
L2Rchain.colnames Source code
L2Rchain.rev Source code
L2Rchain.tagname Source code
L2Rlink Man page Source code
L2Rlink-class Man page
Lkeyname Man page
Lkeyname,AnnDbBimap-method Man page
Lkeyname,Bimap-method Man page
Lkeys Man page
Lkeys,AnnDbBimap-method Man page
Lkeys,FlatBimap-method Man page
Lkeys,ProbeAnnDbBimap-method Man page
Lkeys,ProbeAnnDbMap-method Man page
Lkeys,ProbeGo3AnnDbBimap-method Man page
Lkeys,ProbeIpiAnnDbMap-method Man page
Lkeys<- Man page
Lkeys<-,AnnDbBimap-method Man page
Lkeys<-,FlatBimap-method Man page
Llength Man page
Llength,AnnDbBimap-method Man page
Llength,Bimap-method Man page
Llength,ProbeAnnDbBimap-method Man page
Llength,ProbeAnnDbMap-method Man page
Llength,ProbeGo3AnnDbBimap-method Man page
Llength,ProbeIpiAnnDbMap-method Man page
MAP Man page
NCBICHIP_DB_SeedGenerator Man page Source code
NCBIORG_DB_SeedGenerator Source code
OMIM Man page
ONTOLOGY Man page Man page
ONTOLOGYALL Man page
ORF Man page
Ontology Man page
Ontology,GOTerms-method Man page
Ontology,GOTermsAnnDbBimap-method Man page
Ontology,character-method Man page
OrgDb-class Man page
OrthologyDb-class Man page
PATH Man page
PFAM Man page
PMID Man page
PROBEID Man page
PROSITE Man page
ProbeAnnDbBimap Man page
ProbeAnnDbBimap-class Man page
ProbeAnnDbMap Man page
ProbeAnnDbMap-class Man page
ProbeGo3AnnDbBimap Man page
ProbeGo3AnnDbBimap-class Man page
ProbeIpiAnnDbMap Man page
ProbeIpiAnnDbMap-class Man page
REFSEQ Man page
Rattribnames Man page
Rattribnames,AnnDbBimap-method Man page
Rattribnames,Bimap-method Man page
Rattribnames<- Man page
Rattribnames<-,AnnDbBimap-method Man page
Rattribnames<-,FlatBimap-method Man page
Rattribnames<-,Go3AnnDbBimap-method Man page
ReactomeDb-class Man page
Rkeyname Man page
Rkeyname,AnnDbBimap-method Man page
Rkeyname,Bimap-method Man page
Rkeys Man page
Rkeys,AnnDbBimap-method Man page
Rkeys,AnnDbMap-method Man page
Rkeys,FlatBimap-method Man page
Rkeys,Go3AnnDbBimap-method Man page
Rkeys<- Man page
Rkeys<-,AnnDbBimap-method Man page
Rkeys<-,FlatBimap-method Man page
Rlength Man page
Rlength,AnnDbBimap-method Man page
Rlength,AnnDbMap-method Man page
Rlength,Bimap-method Man page
Rlength,Go3AnnDbBimap-method Man page
SGD Man page
SMART Man page
SYMBOL Man page
Secondary Man page
Secondary,GOTerms-method Man page
Secondary,GOTermsAnnDbBimap-method Man page
Secondary,character-method Man page
Synonym Man page
Synonym,GOTerms-method Man page
Synonym,GOTermsAnnDbBimap-method Man page
Synonym,character-method Man page
TAIR Man page
TERM Man page
Term Man page
Term,GOTerms-method Man page
Term,GOTermsAnnDbBimap-method Man page
Term,character-method Man page
UNIGENE Man page
UNIPROT Man page
[,Bimap-method Man page
[[,Bimap-method Man page
`L2Rchain.Rattribnames<-` Source code
addToNamespaceAndExport Source code
annoStartupMessages Source code
annotMessage Source code
as.character,AnnDbBimap-method Man page
as.character,FlatBimap-method Man page
as.data.frame,Bimap-method Man page
as.data.frame.Bimap Man page Source code
as.list Man page
as.list,AgiAnnDbMap-method Man page
as.list,Bimap-method Man page
as.list,FlatBimap-method Man page
as.list,GOTermsAnnDbBimap-method Man page
as.list,GoAnnDbBimap-method Man page
as.list,IpiAnnDbMap-method Man page
as.list.Bimap Man page Source code
attachDBs Source code
checkDBSCHEMA Source code
checkMAPCOUNTS Man page Source code
checkPROBE2GOmappings Source code
checkProperty0 Source code
chooseCentralOrgPkgSymbol Man page Source code
choosePackage Source code
class:AgiAnnDbMap Man page
class:AnnDbBimap Man page
class:AnnDbMap Man page
class:AnnDbObj Man page
class:AnnObj Man page
class:AnnotationDb Man page
class:Bimap Man page
class:FlatBimap Man page
class:GOAllFrame Man page
class:GOFrame Man page
class:GOTerms Man page
class:GOTermsAnnDbBimap Man page
class:Go3AnnDbBimap Man page
class:GoAnnDbBimap Man page
class:IpiAnnDbMap Man page
class:KEGGFrame Man page
class:L2Rlink Man page
class:ProbeAnnDbBimap Man page
class:ProbeAnnDbMap Man page
class:ProbeGo3AnnDbBimap Man page
class:ProbeIpiAnnDbMap Man page
colmetanames Man page
colmetanames,AnnDbBimap-method Man page
colmetanames,FlatBimap-method Man page
colnames Man page
colnames,AnnDbBimap-method Man page
colnames,FlatBimap-method Man page
cols Man page Source code
columns Man page
columns,AnnotationDb-method Man page
columns,ChipDb-method Man page
columns,GODb-method Man page
columns,Inparanoid8Db-method Man page
columns,InparanoidDb-method Man page
columns,OrgDb-method Man page
columns,OrthologyDb-method Man page
columns,ReactomeDb-method Man page
compareAnnDataIn2Pkgs Source code
contents,Bimap-method Man page
count.links Man page
count.links,Bimap-method Man page
count.links,Go3AnnDbBimap-method Man page
count.mappedLkeys Man page
count.mappedLkeys,AgiAnnDbMap-method Man page
count.mappedLkeys,AnnDbBimap-method Man page
count.mappedLkeys,Bimap-method Man page
count.mappedLkeys,Go3AnnDbBimap-method Man page
count.mappedRkeys Man page
count.mappedRkeys,AnnDbBimap-method Man page
count.mappedRkeys,AnnDbMap-method Man page
count.mappedRkeys,Bimap-method Man page
count.mappedRkeys,Go3AnnDbBimap-method Man page
count.mappedkeys Man page
count.mappedkeys,ANY-method Man page
count.mappedkeys,Bimap-method Man page
createAnnDbBimap Source code
createAnnDbBimaps Source code
createAnnObjs Source code
createAnnObjs.ANOPHELESCHIP_DB Source code
createAnnObjs.ANOPHELES_DB Source code
createAnnObjs.ARABIDOPSISCHIP_DB Source code
createAnnObjs.ARABIDOPSIS_DB Source code
createAnnObjs.BOVINECHIP_DB Source code
createAnnObjs.BOVINE_DB Source code
createAnnObjs.CANINECHIP_DB Source code
createAnnObjs.CANINE_DB Source code
createAnnObjs.CHICKENCHIP_DB Source code
createAnnObjs.CHICKEN_DB Source code
createAnnObjs.CHIMPCHIP_DB Source code
createAnnObjs.CHIMP_DB Source code
createAnnObjs.COELICOLORCHIP_DB Source code
createAnnObjs.COELICOLOR_DB Source code
createAnnObjs.ECOLICHIP_DB Source code
createAnnObjs.ECOLI_DB Source code
createAnnObjs.FLYCHIP_DB Source code
createAnnObjs.FLY_DB Source code
createAnnObjs.GO_DB Source code
createAnnObjs.HUMANCHIP_DB Source code
createAnnObjs.HUMAN_DB Source code
createAnnObjs.KEGG_DB Source code
createAnnObjs.MALARIACHIP_DB Source code
createAnnObjs.MALARIA_DB Source code
createAnnObjs.MOUSECHIP_DB Source code
createAnnObjs.MOUSE_DB Source code
createAnnObjs.NCBI_DB Source code
createAnnObjs.ORGANISM_DB Source code
createAnnObjs.PFAM_DB Source code
createAnnObjs.PIGCHIP_DB Source code
createAnnObjs.PIG_DB Source code
createAnnObjs.RATCHIP_DB Source code
createAnnObjs.RAT_DB Source code
createAnnObjs.RHESUSCHIP_DB Source code
createAnnObjs.RHESUS_DB Source code
createAnnObjs.SchemaChoice Man page Source code
createAnnObjs.WORMCHIP_DB Source code
createAnnObjs.WORM_DB Source code
createAnnObjs.XENOPUSCHIP_DB Source code
createAnnObjs.XENOPUS_DB Source code
createAnnObjs.YEASTCHIP_DB Source code
createAnnObjs.YEASTNCBI_DB Source code
createAnnObjs.YEAST_DB Source code
createAnnObjs.ZEBRAFISHCHIP_DB Source code
createAnnObjs.ZEBRAFISH_DB Source code
createAnnObjs.reactome Source code
createCHRLENGTHS Source code
createMAPCOUNTS Source code
createORGANISMSeeds Source code
createREJECTORF Source code
createSimpleBimap Man page Source code
dbAttach Source code
dbCountRawAnnDbMapRows Source code
dbCountRowsFromL2Rchain Source code
dbCountUniqueMappedKeys Source code
dbCountUniqueVals Source code
dbEasyQuery Source code
dbFileConnect Man page Source code
dbFileDisconnect Man page Source code
dbGetTable Man page Source code
dbInfo Man page
dbInfo,AnnDbObj-method Man page
dbInfo,DBIConnection-method Man page
dbInfo,environment-method Man page
dbObjectName Source code
dbQuery Source code
dbRawAnnDbMapToTable Source code
dbSelectFromL2Rchain Source code
dbUniqueMappedKeys Source code
dbUniqueVals Source code
dbconn Man page
dbconn,AnnDbObj-method Man page
dbconn,AnnotationDb-method Man page
dbconn,SQLiteConnection-method Man page
dbconn,environment-method Man page
dbfile Man page
dbfile,AnnDbObj-method Man page
dbfile,AnnotationDb-method Man page
dbfile,SQLiteConnection-method Man page
dbfile,environment-method Man page
dbmeta Man page
dbmeta,AnnDbObj-method Man page
dbmeta,DBIConnection-method Man page
dbmeta,environment-method Man page
dbschema Man page
dbschema,AnnDbObj-method Man page
dbschema,DBIConnection-method Man page
dbschema,environment-method Man page
debugSQL Man page Source code
dim,Bimap-method Man page
direction Man page
direction,AnnDbBimap-method Man page
direction,FlatBimap-method Man page
direction<- Man page
direction<-,AnnDbBimap-method Man page
direction<-,AnnDbMap-method Man page
direction<-,FlatBimap-method Man page
eapply Man page
eapply,Bimap-method Man page
exists Man page
exists,ANY,ANY,Bimap-method Man page
exists,ANY,Bimap,missing-method Man page
exposeAllProbes Man page
exposeAllProbes,AnnDbBimap-method Man page
filterSeeds Man page Source code
flatten.GO2PROBEenvir Source code
flatten.GOenvir Source code
get Man page
get,ANY,ANY,Bimap-method Man page
get,ANY,Bimap,missing-method Man page
getBimapFilters Man page
getBimapFilters,AnnDbBimap-method Man page
getDBMaps Source code
getGOFrameData Man page
getGOFrameData,GOAllFrame-method Man page
getGOFrameData,GOFrame-method Man page
getKEGGFrameData Man page
getKEGGFrameData,KEGGAllFrame-method Man page
getKEGGFrameData,KEGGFrame-method Man page
getOrgPkgForSchema Man page Source code
getSpeciesFromSchema Source code
hasMultiProbes Man page
hasMultiProbes,ProbeAnnDbBimap-method Man page
hasMultiProbes,ProbeAnnDbMap-method Man page
hasMultiProbes,ProbeGo3AnnDbBimap-method Man page
hasMultiProbes,ProbeIpiAnnDbMap-method Man page
hasSingleProbes Man page
hasSingleProbes,ProbeAnnDbBimap-method Man page
hasSingleProbes,ProbeAnnDbMap-method Man page
hasSingleProbes,ProbeGo3AnnDbBimap-method Man page
hasSingleProbes,ProbeIpiAnnDbMap-method Man page
head,FlatBimap-method Man page
idConverter Man page Source code
identical.collections Source code
identical.uulists Source code
initialize,FlatBimap-method Man page
initialize,GOTerms-method Man page
initialize,L2Rlink-method Man page
inpIDMapper Man page Source code
intraIDMapper Man page Source code
isNA Man page
isNA,ANY-method Man page
isNA,Bimap-method Man page
isNA,environment-method Man page
keyname Man page
keyname,Bimap-method Man page
keys Man page Man page
keys,AnnotationDb-method Man page
keys,Bimap-method Man page
keys,ChipDb-method Man page
keys,GODb-method Man page
keys,Inparanoid8Db-method Man page
keys,InparanoidDb-method Man page
keys,OrgDb-method Man page
keys,OrthologyDb-method Man page
keys,ReactomeDb-method Man page
keys<- Man page
keys<-,Bimap-method Man page
keytypes Man page
keytypes,ChipDb-method Man page
keytypes,GODb-method Man page
keytypes,Inparanoid8Db-method Man page
keytypes,InparanoidDb-method Man page
keytypes,OrgDb-method Man page
keytypes,OrthologyDb-method Man page
keytypes,ReactomeDb-method Man page
length,Bimap-method Man page
links Man page
links,AnnDbBimap-method Man page
links,Bimap-method Man page
links,FlatBimap-method Man page
links,Go3AnnDbBimap-method Man page
loadDb Man page Source code
ls Man page
ls,Bimap-method Man page
make.name.tree Source code
makeAnnDbBiMapSeed Source code
makeFlatBimapUsingSelect Source code
makeGOGraph Man page Source code
makeGo3AnnDbBiMapSeed Source code
makeGo3L2Rchain Source code
make_eg_to_go_map Man page Source code
make_go_to_eg_map Man page Source code
mapIds Man page
mapIds,AnnotationDb-method Man page
mapIds_base Man page Source code
mappedLkeys Man page
mappedLkeys,AgiAnnDbMap-method Man page
mappedLkeys,AnnDbBimap-method Man page
mappedLkeys,FlatBimap-method Man page
mappedLkeys,Go3AnnDbBimap-method Man page
mappedLkeysIsNotAvailable Source code
mappedRkeys Man page
mappedRkeys,AnnDbBimap-method Man page
mappedRkeys,AnnDbMap-method Man page
mappedRkeys,FlatBimap-method Man page
mappedRkeys,Go3AnnDbBimap-method Man page
mappedkeys Man page
mappedkeys,Bimap-method Man page
mappedkeys,environment-method Man page
mappedkeys,vector-method Man page
maskMultiProbes Man page
maskMultiProbes,AnnDbBimap-method Man page
maskSingleProbes Man page
maskSingleProbes,AnnDbBimap-method Man page
mergeToNamespaceAndExport Man page Source code
metadata,AnnotationDb-method Man page
mget Man page
mget,ANY,Bimap-method Man page
mget,Bimap-method Man page
names,AnnotationDb-method Man page
ncol Man page
ncol,Bimap-method Man page
nhit Man page
nhit,Bimap-method Man page
nhit,environment-method Man page
nhit,list-method Man page
nrow Man page
nrow,AnnDbBimap-method Man page
nrow,AnnDbTable-method Man page
nrow,Bimap-method Man page
nrow,FlatBimap-method Man page
nrow,Go3AnnDbBimap-method Man page
orgPackageName Man page
organismKEGGFrame Man page Man page Source code
prefixAnnObjNames Source code
print.probetable Man page Source code
resort_base Man page Source code
revmap Man page
revmap,AnnDbBimap-method Man page
revmap,Bimap-method Man page
revmap,environment-method Man page
revmap,list-method Man page
sample Man page
sample,Bimap-method Man page
sample,environment-method Man page
saveDb Man page
saveDb,AnnotationDb-method Man page
select Man page
select,AnnotationDb-method Man page
select,ChipDb-method Man page
select,GODb-method Man page
select,Inparanoid8Db-method Man page
select,InparanoidDb-method Man page
select,OrgDb-method Man page
select,OrthologyDb-method Man page
select,ReactomeDb-method Man page
show,AnnDbBimap-method Man page
show,AnnDbTable-method Man page
show,AnnotationDb-method Man page
show,FlatBimap-method Man page
show,GOTerms-method Man page
show,L2Rlink-method Man page
showQCData Man page Source code
smartKeys Source code
species Man page
species,AnnotationDb-method Man page
subset,AnnDbBimap-method Man page
subset,Bimap-method Man page
summary,AnnDbBimap-method Man page
summary,Bimap-method Man page
tagname Man page
tagname,AnnDbBimap-method Man page
tagname,Bimap-method Man page
tail,FlatBimap-method Man page
taxonomyId Man page
taxonomyId,AnnotationDb-method Man page
testForValidKeytype Man page Source code
testSelectArgs Man page Source code
toSQLStringSet Man page
toTable Man page
toTable,Bimap-method Man page
toTable,FlatBimap-method Man page
toggleProbes Man page
toggleProbes,ProbeAnnDbBimap-method Man page
toggleProbes,ProbeAnnDbMap-method Man page
toggleProbes,ProbeGo3AnnDbBimap-method Man page
toggleProbes,ProbeIpiAnnDbMap-method Man page
unlist2 Man page Source code
jmacdon/AnnotationDbi documentation built on Oct. 22, 2021, 9:14 p.m.

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