# Annotation Database Interface

## Documentation for package ‘AnnotationDbi’ version 1.16.19

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

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

## -- 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
AnnotationDb | AnnotationDb objects and their progeny, methods etc.
AnnotationDb-class | AnnotationDb objects and their progeny, methods etc.
as.character-method | Formatting a Bimap as a list or character vector
as.data.frame-method | Methods for manipulating a Bimap object in a data-frame style
as.list | Formatting a Bimap as a list or character vector
as.list-method | Formatting a Bimap as a list or character vector
available.chipdbschemas | available.db0pkgs
available.db0pkgs | available.db0pkgs
available.dbschemas | available.db0pkgs

## -- 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
buildEntrezGeneDbFromWebServices | builds an Entrez Gene centric organism database

## -- 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:AnnotationDb | AnnotationDb objects and their progeny, methods etc.
class:Bimap | Bimap objects and the Bimap interface
class:Go3AnnDbBimap | Bimap objects and the Bimap interface
class:GOAllFrame | GOFrame and GOAllFrame objects
class:GoAnnDbBimap | Bimap objects and the Bimap interface
class:GOFrame | GOFrame and GOAllFrame objects
class:GOTerms | Class "GOTerms"
class:GOTermsAnnDbBimap | Bimap objects and the Bimap interface
class:IpiAnnDbMap | Bimap objects and the Bimap interface
class:KEGGFrame | KEGGFrame objects
class:ProbeAnnDbBimap | Bimap objects and the Bimap interface
class:ProbeAnnDbMap | Bimap objects and the Bimap interface
class:ProbeGo3AnnDbBimap | Bimap objects and the Bimap interface
class:ProbeIpiAnnDbMap | Bimap objects and the Bimap interface
colmetanames | Methods for manipulating a Bimap object in a data-frame style
colmetanames-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-method | Methods for manipulating a Bimap object in a data-frame style
cols | AnnotationDb objects and their progeny, methods etc.
cols-method | AnnotationDb objects and their progeny, methods etc.
contents-method | Environment-like API for AnnDbBimap objects
count.links | Methods for manipulating a Bimap object in a data-frame style
count.links-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-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-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-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
createSimpleBimap | Creates a simple Bimap from a SQLite database in an situation that is external to AnnotationDbi

## -- D --

dbconn | AnnDbObj objects
dbConn-method | AnnotationDb objects and their progeny, methods etc.
dbconn-method | AnnDbObj objects
dbfile | AnnDbObj objects
dbfile-method | AnnDbObj objects
dbInfo | AnnDbObj objects
dbInfo-method | AnnDbObj objects
dbmeta | AnnDbObj objects
dbmeta-method | AnnDbObj objects
dbschema | AnnDbObj objects
dbschema-method | AnnDbObj objects
Definition | Class "GOTerms"
Definition-method | Class "GOTerms"
dim-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-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
direction<- | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
direction<--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-method | Environment-like API for AnnDbBimap objects
exists | Environment-like API for AnnDbBimap objects
exists-method | Environment-like API for AnnDbBimap objects

## -- G --

get | Environment-like API for AnnDbBimap objects
get-method | Environment-like API for AnnDbBimap objects
getBimapFilters | Methods for getting/setting the filters on a Bimap object
getBimapFilters-method | Methods for getting/setting the filters on a Bimap object
getEntrezGenesFromTaxId | builds an Entrez Gene centric organism database
getGeneStuff | builds an Entrez Gene centric organism database
getGOFrameData | GOFrame and GOAllFrame objects
getGOFrameData-method | GOFrame and GOAllFrame objects
getKEGGFrameData | KEGGFrame objects
getKEGGFrameData-method | KEGGFrame objects
getProbeDataAffy | Read a data file describing the probe sequences on an Affymetrix genechip
getProbeData_1lq | Read a 1lq file for an Affymetrix genechip
Go3AnnDbBimap | Bimap objects and the Bimap interface
Go3AnnDbBimap-class | Bimap objects and the Bimap interface
GOAllFrame | GOFrame and GOAllFrame objects
GOAllFrame-class | GOFrame and GOAllFrame objects
GOAllFrame-method | GOFrame and GOAllFrame objects
GoAnnDbBimap | Bimap objects and the Bimap interface
GoAnnDbBimap-class | Bimap objects and the Bimap interface
GOFrame | GOFrame and GOAllFrame objects
GOFrame-class | GOFrame and GOAllFrame objects
GOFrame-method | GOFrame and GOAllFrame objects
GOID | Class "GOTerms"
GOID-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 --

hasMultiProbes | Methods for getting/setting the filters on a Bimap object
hasMultiProbes-method | Methods for getting/setting the filters on a Bimap object
hasSingleProbes | Methods for getting/setting the filters on a Bimap object
hasSingleProbes-method | Methods for getting/setting the filters on a Bimap object
head | Methods for manipulating a Bimap object in a data-frame style
head-method | Methods for manipulating a Bimap object in a data-frame style

## -- I --

idConverter | Convenience functions for mapping IDs through an appropriate set of annotation packages
initialize-method | Class "GOTerms"
inpIDMapper | Convenience functions for mapping IDs through an appropriate set of annotation packages
intraIDMapper | Convenience functions for mapping IDs through an appropriate set of annotation packages
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-method | Methods for manipulating the keys of a Bimap object

## -- K --

KEGGFrame | KEGGFrame objects
KEGGFrame-class | KEGGFrame objects
KEGGFrame-method | KEGGFrame objects
keyname | Methods for manipulating a Bimap object in a data-frame style
keyname-method | Methods for manipulating a Bimap object in a data-frame style
keys | Methods for manipulating the keys of a Bimap object
keys-method | AnnotationDb objects and their progeny, methods etc.
keys-method | Methods for manipulating the keys of a Bimap object
keys<- | Methods for manipulating the keys of a Bimap object
keys<--method | Methods for manipulating the keys of a Bimap object
keytypes | AnnotationDb objects and their progeny, methods etc.
keytypes-method | AnnotationDb objects and their progeny, methods etc.

## -- L --

length-method | Methods for manipulating the keys of a Bimap object
links | Methods for manipulating a Bimap object in a data-frame style
links-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-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-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Lkeys<- | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Lkeys<--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-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
loadDb | AnnotationDb objects and their progeny, methods etc.
loadDb-method | AnnotationDb objects and their progeny, methods etc.
ls | Environment-like API for AnnDbBimap objects
ls-method | Environment-like API for AnnDbBimap objects

## -- M --

makeAnnDbPkg | Creates an SQLite-based annotation package
makeAnnDbPkg-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
makeDBPackage | 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
makeOrgPackageFromBiomart | Making an organism package from annotations available from NCBI.
makeOrgPackageFromNCBI | Making an organism package from annotations available from NCBI.
makePIGCHIP_DB | Creates a sqlite database, and then makes an annotation package with it
makeProbePackage | Make a package with probe sequence related data for microarrays
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-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-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-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
metadata-method | AnnotationDb objects and their progeny, methods etc.
mget | Environment-like API for AnnDbBimap objects
mget-method | Environment-like API for AnnDbBimap objects

## -- N --

names-method | AnnotationDb objects and their progeny, methods etc.
ncol | Methods for manipulating a Bimap object in a data-frame style
ncol-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-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-method | Methods for manipulating a Bimap object in a data-frame style

## -- O --

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

## -- P --

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
populateDB | 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
popYEASTDB | Populates an SQLite DB with and produces a schema definition
popYEASTNCBIDB | 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
print.probetable | Print method for probetable objects
ProbeAnnDbBimap | Bimap objects and the Bimap interface
ProbeAnnDbBimap-class | Bimap objects and the Bimap interface
ProbeAnnDbMap | Bimap objects and the Bimap interface
ProbeAnnDbMap-class | Bimap objects and the Bimap interface
ProbeGo3AnnDbBimap | Bimap objects and the Bimap interface
ProbeGo3AnnDbBimap-class | Bimap objects and the Bimap interface
ProbeIpiAnnDbMap | Bimap objects and the Bimap interface
ProbeIpiAnnDbMap-class | Bimap objects and the Bimap interface

## -- R --

Rattribnames | Methods for manipulating a Bimap object in a data-frame style
Rattribnames-method | Methods for manipulating a Bimap object in a data-frame style
Rattribnames<- | Methods for manipulating a Bimap object in a data-frame style
Rattribnames<--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-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-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-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rkeys<- | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
Rkeys<--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-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-method | Environment-like API for AnnDbBimap objects
saveDb | AnnotationDb objects and their progeny, methods etc.
saveDb-method | AnnotationDb objects and their progeny, methods etc.
Secondary | Class "GOTerms"
Secondary-method | Class "GOTerms"
select | AnnotationDb objects and their progeny, methods etc.
select-method | AnnotationDb objects and their progeny, methods etc.
setInpBimapFilter | Methods for getting/setting the filters on a Bimap object
setInpBimapFilter-method | Methods for getting/setting the filters on a Bimap object
show-method | AnnotationDb objects and their progeny, methods etc.
show-method | Methods for manipulating the keys of a Bimap object
show-method | Bimap objects and the Bimap interface
show-method | Class "GOTerms"
subset | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
subset-method | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys
summary-method | Bimap objects and the Bimap interface
Synonym | Class "GOTerms"
Synonym-method | Class "GOTerms"

## -- T --

tagname | Methods for manipulating a Bimap object in a data-frame style
tagname-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-method | Methods for manipulating a Bimap object in a data-frame style
Term | Class "GOTerms"
Term-method | Class "GOTerms"
toggleProbes | Methods for getting/setting the filters on a Bimap object
toggleProbes-method | Methods for getting/setting the filters on a Bimap object
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-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 --

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