# Annotation Database Interface

## Documentation for package ‘AnnotationDbi’ version 1.4.3

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D E G H I K L M N O P R S T U W misc

$,AnnDbBimap-method | Environment-like API for AnnDbBimap objects

## -- A --

AgiAnnDbMap | Bimap objects and the Bimap interface
AgiAnnDbMap-class | Bimap objects and the Bimap interface
AnnDbBimap | Bimap objects and the Bimap interface
AnnDbBimap-class | Bimap objects and the Bimap interface
AnnDbBimap-envirAPI | Environment-like API for AnnDbBimap objects
AnnDbMap | Bimap objects and the Bimap interface
AnnDbMap-class | Bimap objects and the Bimap interface
AnnDbObj | AnnDbObj objects
AnnDbObj-class | AnnDbObj objects
AnnDbObj-objects | AnnDbObj objects
AnnDbPkg-checker | Check the SQL data contained in an SQLite-based annotation package
AnnDbPkg-maker | Creates an SQLite-based annotation package
AnnDbPkgSeed | Creates an SQLite-based annotation package
AnnDbPkgSeed-class | Creates an SQLite-based annotation package
as.character,AnnDbBimap-method | Formatting a Bimap as a list or character vector
as.list | Formatting a Bimap as a list or character vector
as.list,AgiAnnDbMap-method | Formatting a Bimap as a list or character vector
as.list,AnnDbBimap-method | Formatting a Bimap as a list or character vector
as.list,Bimap-method | Formatting a Bimap as a list or character vector
as.list,GoAnnDbBimap-method | Formatting a Bimap as a list or character vector
as.list,GOTermsAnnDbBimap-method | Formatting a Bimap as a list or character vector
as.list,IpiAnnDbMap-method | Formatting a Bimap as a list or character vector

## -- B --

Bimap | Bimap objects and the Bimap interface
Bimap-class | Bimap objects and the Bimap interface
Bimap-direction | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Bimap-keys | Methods for manipulating the keys of a Bimap object
Bimap-toTable | Methods for manipulating a Bimap object in a data-frame style
BimapFormatting | Formatting a Bimap as a list or character vector

## -- C --

checkMAPCOUNTS | Check the SQL data contained in an SQLite-based annotation package
class:AgiAnnDbMap | Bimap objects and the Bimap interface
class:AnnDbBimap | Bimap objects and the Bimap interface
class:AnnDbMap | Bimap objects and the Bimap interface
class:AnnDbObj | AnnDbObj objects
class:AnnDbPkgSeed | Creates an SQLite-based annotation package
class:Bimap | Bimap objects and the Bimap interface
class:Go3AnnDbBimap | Bimap objects and the Bimap interface
class:GoAnnDbBimap | Bimap objects and the Bimap interface
class:GOTerms | Class "GOTerms"
class:GOTermsAnnDbBimap | Bimap objects and the Bimap interface
class:IpiAnnDbMap | Bimap objects and the Bimap interface
colmetanames | Methods for manipulating a Bimap object in a data-frame style
colmetanames,AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
colmetanames,FlatBimap-method | Methods for manipulating a Bimap object in a data-frame style
colnames | Methods for manipulating a Bimap object in a data-frame style
colnames,AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
colnames,FlatBimap-method | Methods for manipulating a Bimap object in a data-frame style
contents,Bimap-method | Environment-like API for AnnDbBimap objects
count.links | Methods for manipulating a Bimap object in a data-frame style
count.links,Bimap-method | Methods for manipulating a Bimap object in a data-frame style
count.links,Go3AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
count.mappedkeys | Methods for manipulating the keys of a Bimap object
count.mappedkeys,ANY-method | Methods for manipulating the keys of a Bimap object
count.mappedkeys,Bimap-method | Methods for manipulating the keys of a Bimap object
count.mappedLkeys | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
count.mappedLkeys,AgiAnnDbMap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
count.mappedLkeys,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
count.mappedLkeys,Bimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
count.mappedLkeys,Go3AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
count.mappedRkeys | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
count.mappedRkeys,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
count.mappedRkeys,AnnDbMap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
count.mappedRkeys,Bimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
count.mappedRkeys,Go3AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys

## -- D --

dbconn | AnnDbObj objects
dbconn,AnnDbObj-method | AnnDbObj objects
dbconn,environment-method | AnnDbObj objects
dbfile | AnnDbObj objects
dbfile,AnnDbObj-method | AnnDbObj objects
dbfile,environment-method | AnnDbObj objects
dbInfo | AnnDbObj objects
dbInfo,AnnDbObj-method | AnnDbObj objects
dbInfo,DBIConnection-method | AnnDbObj objects
dbInfo,environment-method | AnnDbObj objects
dbmeta | AnnDbObj objects
dbmeta,AnnDbObj-method | AnnDbObj objects
dbmeta,DBIConnection-method | AnnDbObj objects
dbmeta,environment-method | AnnDbObj objects
dbschema | AnnDbObj objects
dbschema,AnnDbObj-method | AnnDbObj objects
dbschema,DBIConnection-method | AnnDbObj objects
dbschema,environment-method | AnnDbObj objects
Definition | Class "GOTerms"
Definition,GOTerms-method | Class "GOTerms"
dim,Bimap-method | Methods for manipulating a Bimap object in a data-frame style
direction | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
direction,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
direction,FlatBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
direction<-,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
direction<-,AnnDbMap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
direction<-,FlatBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys

## -- E --

eapply | Environment-like API for AnnDbBimap objects
eapply,Bimap-method | Environment-like API for AnnDbBimap objects
exists | Environment-like API for AnnDbBimap objects
exists,ANY,ANY,Bimap-method | Environment-like API for AnnDbBimap objects
exists,ANY,Bimap,missing-method | Environment-like API for AnnDbBimap objects

## -- G --

get | Environment-like API for AnnDbBimap objects
get,ANY,AnnDbBimap,missing-method | Environment-like API for AnnDbBimap objects
get,ANY,ANY,AnnDbBimap-method | Environment-like API for AnnDbBimap objects
Go3AnnDbBimap | Bimap objects and the Bimap interface
Go3AnnDbBimap-class | Bimap objects and the Bimap interface
GoAnnDbBimap | Bimap objects and the Bimap interface
GoAnnDbBimap-class | Bimap objects and the Bimap interface
GOID | Class "GOTerms"
GOID,GOTerms-method | Class "GOTerms"
GOTerms | Class "GOTerms"
GOTerms-class | Class "GOTerms"
GOTermsAnnDbBimap | Bimap objects and the Bimap interface
GOTermsAnnDbBimap-class | Bimap objects and the Bimap interface

## -- H --

head | Methods for manipulating a Bimap object in a data-frame style
head,FlatBimap-method | Methods for manipulating a Bimap object in a data-frame style

## -- I --

initialize,GOTerms-method | Class "GOTerms"
IpiAnnDbMap | Bimap objects and the Bimap interface
IpiAnnDbMap-class | Bimap objects and the Bimap interface
isNA | Methods for manipulating the keys of a Bimap object
isNA,ANY-method | Methods for manipulating the keys of a Bimap object
isNA,Bimap-method | Methods for manipulating the keys of a Bimap object
isNA,environment-method | Methods for manipulating the keys of a Bimap object

## -- K --

keyname | Methods for manipulating a Bimap object in a data-frame style
keyname,Bimap-method | Methods for manipulating a Bimap object in a data-frame style
keys | Methods for manipulating the keys of a Bimap object
keys,Bimap-method | Methods for manipulating the keys of a Bimap object
keys<-,Bimap-method | Methods for manipulating the keys of a Bimap object

## -- L --

length,Bimap-method | Methods for manipulating the keys of a Bimap object
links | Methods for manipulating a Bimap object in a data-frame style
links,AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
links,FlatBimap-method | Methods for manipulating a Bimap object in a data-frame style
links,Go3AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
Lkeyname | Methods for manipulating a Bimap object in a data-frame style
Lkeyname,AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
Lkeyname,Bimap-method | Methods for manipulating a Bimap object in a data-frame style
Lkeys | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Lkeys,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Lkeys,FlatBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Lkeys<-,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Lkeys<-,FlatBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Llength | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Llength,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Llength,Bimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
loadAnnDbPkgIndex | Creates an SQLite-based annotation package
ls | Environment-like API for AnnDbBimap objects
ls,Bimap-method | Environment-like API for AnnDbBimap objects

## -- M --

makeAnnDbPkg | Creates an SQLite-based annotation package
makeAnnDbPkg,AnnDbPkgSeed-method | Creates an SQLite-based annotation package
makeAnnDbPkg,character-method | Creates an SQLite-based annotation package
makeAnnDbPkg,list-method | Creates an SQLite-based annotation package
makeARABIDOPSISCHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makeBOVINECHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makeCANINECHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makeCHICKENCHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makeECOLICHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makeFLYCHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makeHUMANCHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makeMOUSECHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makePIGCHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makeRATCHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makeWORMCHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makeYEASTCHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makeZEBRAFISHCHIP_DB | Creates a sqlite database, and then makes an annotation package with it
make_eg_to_go_map | Create GO to Entrez Gene maps for chip-based packages
make_go_to_eg_map | Create GO to Entrez Gene maps for chip-based packages
mappedkeys | Methods for manipulating the keys of a Bimap object
mappedkeys,Bimap-method | Methods for manipulating the keys of a Bimap object
mappedkeys,environment-method | Methods for manipulating the keys of a Bimap object
mappedkeys,vector-method | Methods for manipulating the keys of a Bimap object
mappedLkeys | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
mappedLkeys,AgiAnnDbMap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
mappedLkeys,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
mappedLkeys,FlatBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
mappedLkeys,Go3AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
mappedRkeys | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
mappedRkeys,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
mappedRkeys,AnnDbMap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
mappedRkeys,FlatBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
mappedRkeys,Go3AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
mget | Environment-like API for AnnDbBimap objects
mget,AnnDbBimap-method | Environment-like API for AnnDbBimap objects
mget,ANY,AnnDbBimap-method | Environment-like API for AnnDbBimap objects

## -- N --

ncol | Methods for manipulating a Bimap object in a data-frame style
ncol,Bimap-method | Methods for manipulating a Bimap object in a data-frame style
nhit | Methods for manipulating a Bimap object in a data-frame style
nhit,Bimap-method | Methods for manipulating a Bimap object in a data-frame style
nhit,environment-method | Methods for manipulating a Bimap object in a data-frame style
nhit,list-method | Methods for manipulating a Bimap object in a data-frame style
nrow | Methods for manipulating a Bimap object in a data-frame style
nrow,AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
nrow,AnnDbTable-method | Methods for manipulating a Bimap object in a data-frame style
nrow,FlatBimap-method | Methods for manipulating a Bimap object in a data-frame style
nrow,Go3AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style

## -- O --

Ontology | Class "GOTerms"
Ontology,GOTerms-method | Class "GOTerms"

## -- P --

popARABIDOPSISCHIPDB | Populates an SQLite DB with and produces a schema definition
popBOVINECHIPDB | Populates an SQLite DB with and produces a schema definition
popBOVINEDB | Populates an SQLite DB with and produces a schema definition
popCANINECHIPDB | Populates an SQLite DB with and produces a schema definition
popCANINEDB | Populates an SQLite DB with and produces a schema definition
popCHICKENCHIPDB | Populates an SQLite DB with and produces a schema definition
popCHICKENDB | Populates an SQLite DB with and produces a schema definition
popECOLICHIPDB | Populates an SQLite DB with and produces a schema definition
popECOLIDB | Populates an SQLite DB with and produces a schema definition
popFLYCHIPDB | Populates an SQLite DB with and produces a schema definition
popFLYDB | Populates an SQLite DB with and produces a schema definition
popHUMANCHIPDB | Populates an SQLite DB with and produces a schema definition
popHUMANDB | Populates an SQLite DB with and produces a schema definition
popMALARIADB | Populates an SQLite DB with and produces a schema definition
popMOUSECHIPDB | Populates an SQLite DB with and produces a schema definition
popMOUSEDB | Populates an SQLite DB with and produces a schema definition
popPIGCHIPDB | Populates an SQLite DB with and produces a schema definition
popPIGDB | Populates an SQLite DB with and produces a schema definition
popRATCHIPDB | Populates an SQLite DB with and produces a schema definition
popRATDB | Populates an SQLite DB with and produces a schema definition
popWORMCHIPDB | Populates an SQLite DB with and produces a schema definition
popWORMDB | Populates an SQLite DB with and produces a schema definition
popYEASTCHIPDB | Populates an SQLite DB with and produces a schema definition
popYEASTDB | Populates an SQLite DB with and produces a schema definition
popZEBRAFISHCHIPDB | Populates an SQLite DB with and produces a schema definition
popZEBRAFISHDB | Populates an SQLite DB with and produces a schema definition

## -- R --

Rattribnames | Methods for manipulating a Bimap object in a data-frame style
Rattribnames,AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
Rattribnames,Bimap-method | Methods for manipulating a Bimap object in a data-frame style
Rattribnames<-,AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
Rattribnames<-,FlatBimap-method | Methods for manipulating a Bimap object in a data-frame style
Rattribnames<-,Go3AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
revmap | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
revmap,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
revmap,Bimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
revmap,environment-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
revmap,list-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rkeyname | Methods for manipulating a Bimap object in a data-frame style
Rkeyname,AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
Rkeyname,Bimap-method | Methods for manipulating a Bimap object in a data-frame style
Rkeys | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rkeys,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rkeys,AnnDbMap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rkeys,FlatBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rkeys,Go3AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rkeys<-,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rkeys<-,FlatBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rlength | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rlength,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rlength,AnnDbMap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rlength,Bimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rlength,Go3AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys

## -- S --

sample | Environment-like API for AnnDbBimap objects
sample,Bimap-method | Environment-like API for AnnDbBimap objects
sample,environment-method | Environment-like API for AnnDbBimap objects
Secondary | Class "GOTerms"
Secondary,GOTerms-method | Class "GOTerms"
show,AnnDbBimap-method | Bimap objects and the Bimap interface
show,AnnDbTable-method | Methods for manipulating the keys of a Bimap object
show,FlatBimap-method | Bimap objects and the Bimap interface
show,GOTerms-method | Class "GOTerms"
subset | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
subset,AnnDbBimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
subset,Bimap-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
summary,AnnDbBimap-method | Bimap objects and the Bimap interface
summary,Bimap-method | Bimap objects and the Bimap interface
Synonym | Class "GOTerms"
Synonym,GOTerms-method | Class "GOTerms"

## -- T --

tagname | Methods for manipulating a Bimap object in a data-frame style
tagname,AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
tagname,Bimap-method | Methods for manipulating a Bimap object in a data-frame style
tail | Methods for manipulating a Bimap object in a data-frame style
tail,FlatBimap-method | Methods for manipulating a Bimap object in a data-frame style
Term | Class "GOTerms"
Term,GOTerms-method | Class "GOTerms"
toSQLStringSet | Convert a vector to a quoted string for use as a SQL value list
toTable | Methods for manipulating a Bimap object in a data-frame style
toTable,AnnDbBimap-method | Methods for manipulating a Bimap object in a data-frame style
toTable,FlatBimap-method | Methods for manipulating a Bimap object in a data-frame style

## -- U --

unlist2 | A replacement for unlist() that does not mangle the names

## -- W --

wrapBaseDBPackages | Wrap up all the Base Databases into Packages for distribution

## -- misc --

[,Bimap-method | Methods for manipulating the keys of a Bimap object
[[,AnnDbBimap-method | Environment-like API for AnnDbBimap objects