# Manipulation of SQLite-based annotations in Bioconductor

## Documentation for package ‘AnnotationDbi’ version 1.60.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

## -- A --

ACCNUM | Descriptions of available values for 'columns' and 'keytypes'.
AgiAnnDbMap | Bimap objects and the Bimap interface
AgiAnnDbMap-class | Bimap objects and the Bimap interface
ALIAS | Descriptions of available values for 'columns' and 'keytypes'.
AnnDbBimap | Bimap objects and the Bimap interface
AnnDbBimap-class | Bimap objects and the Bimap interface
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
AnnotationDb | AnnotationDb objects and their progeny, methods etc.
AnnotationDb-class | AnnotationDb objects and their progeny, methods etc.
ARACYC | Descriptions of available values for 'columns' and 'keytypes'.
ARACYCENZYME | Descriptions of available values for 'columns' and 'keytypes'.
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.data.frame.Bimap | 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
as.list.Bimap | 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-envirAPI | Environment-like API for Bimap objects
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
ChipDb-class | AnnotationDb objects and their progeny, methods etc.
CHR | Descriptions of available values for 'columns' and 'keytypes'.
CHRLOC | Descriptions of available values for 'columns' and 'keytypes'.
CHRLOCEND | Descriptions of available values for 'columns' and 'keytypes'.
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: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.
columns | AnnotationDb objects and their progeny, methods etc.
columns-method | AnnotationDb objects and their progeny, methods etc.
COMMON | Descriptions of available values for 'columns' and 'keytypes'.
contents-method | Environment-like API for Bimap 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 | AnnDbObj objects
dbconn-method | AnnotationDb objects and their progeny, methods etc.
dbfile | AnnDbObj objects
dbfile-method | AnnDbObj objects
dbfile-method | AnnotationDb objects and their progeny, methods etc.
dbInfo | AnnDbObj objects
dbInfo-method | AnnDbObj objects
dbmeta | AnnDbObj objects
dbmeta-method | AnnDbObj objects
dbschema | AnnDbObj objects
dbschema-method | AnnDbObj objects
DEFINITION | Descriptions of available values for 'columns' and 'keytypes' for GO.db.
Definition | Class "GOTerms"
Definition-method | Class "GOTerms"
DESCRIPTION | Descriptions of available values for 'columns' and 'keytypes'.
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 Bimap objects
eapply-method | Environment-like API for Bimap objects
ENSEMBL | Descriptions of available values for 'columns' and 'keytypes'.
ENSEMBLPROT | Descriptions of available values for 'columns' and 'keytypes'.
ENSEMBLTRANS | Descriptions of available values for 'columns' and 'keytypes'.
ENTREZID | Descriptions of available values for 'columns' and 'keytypes'.
ENZYME | Descriptions of available values for 'columns' and 'keytypes'.
EVIDENCE | Descriptions of available values for 'columns' and 'keytypes'.
EVIDENCEALL | Descriptions of available values for 'columns' and 'keytypes'.
exists | Environment-like API for Bimap objects
exists-method | Environment-like API for Bimap objects

## -- G --

GENENAME | Descriptions of available values for 'columns' and 'keytypes'.
get | Environment-like API for Bimap objects
get-method | Environment-like API for Bimap objects
getBimapFilters | Methods for getting/setting the filters on a Bimap object
getBimapFilters-method | Methods for getting/setting the filters on a Bimap object
getGOFrameData | GOFrame and GOAllFrame objects
getGOFrameData-method | GOFrame and GOAllFrame objects
getKEGGFrameData | KEGGFrame objects
getKEGGFrameData-method | KEGGFrame objects
GO | Descriptions of available values for 'columns' and 'keytypes'.
Go3AnnDbBimap | Bimap objects and the Bimap interface
Go3AnnDbBimap-class | Bimap objects and the Bimap interface
GOALL | Descriptions of available values for 'columns' and 'keytypes'.
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
GODb-class | AnnotationDb objects and their progeny, methods etc.
GOFrame | GOFrame and GOAllFrame objects
GOFrame-class | GOFrame and GOAllFrame objects
GOFrame-method | GOFrame and GOAllFrame objects
GOID | Descriptions of available values for 'columns' and 'keytypes' for GO.db.
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-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"
InparanoidDb-class | AnnotationDb objects and their progeny, methods etc.
inpIDMapper | Convenience functions for mapping IDs through an appropriate set of annotation packages
INTERPRO | Descriptions of available values for 'columns' and 'keytypes'.
intraIDMapper | Convenience functions for mapping IDs through an appropriate set of annotation packages
IPI | Descriptions of available values for 'columns' and 'keytypes'.
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 | AnnotationDb objects and their progeny, methods etc.
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
loadDb | AnnotationDb objects and their progeny, methods etc.
ls | Environment-like API for Bimap objects
ls-method | Environment-like API for Bimap objects

## -- M --

makeGOGraph | A convenience function to generate graphs based on the GO.db package
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
MAP | Descriptions of available values for 'columns' and 'keytypes'.
mapIds | AnnotationDb objects and their progeny, methods etc.
mapIds-method | AnnotationDb objects and their progeny, methods etc.
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 Bimap objects
mget-method | Environment-like API for Bimap 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 --

OMIM | Descriptions of available values for 'columns' and 'keytypes'.
ONTOLOGY | Descriptions of available values for 'columns' and 'keytypes' for GO.db.
Ontology | Class "GOTerms"
Ontology-method | Class "GOTerms"
ONTOLOGYALL | Descriptions of available values for 'columns' and 'keytypes'.
ORF | Descriptions of available values for 'columns' and 'keytypes'.
organismKEGGFrame | A data frame that maps species names to KEGG organisms
OrgDb-class | AnnotationDb objects and their progeny, methods etc.
orgPackageName | Org package contained in annotation object
OrthologyDb-class | AnnotationDb objects and their progeny, methods etc.

## -- P --

PATH | Descriptions of available values for 'columns' and 'keytypes'.
PFAM | Descriptions of available values for 'columns' and 'keytypes'.
PMID | Descriptions of available values for 'columns' and 'keytypes'.
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
PROBEID | Descriptions of available values for 'columns' and 'keytypes'.
ProbeIpiAnnDbMap | Bimap objects and the Bimap interface
ProbeIpiAnnDbMap-class | Bimap objects and the Bimap interface
PROSITE | Descriptions of available values for 'columns' and 'keytypes'.

## -- 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
ReactomeDb-class | AnnotationDb objects and their progeny, methods etc.
REFSEQ | Descriptions of available values for 'columns' and 'keytypes'.
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 Bimap objects
sample-method | Environment-like API for Bimap 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.
SGD | Descriptions of available values for 'columns' and 'keytypes'.
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"
SMART | Descriptions of available values for 'columns' and 'keytypes'.
species | AnnotationDb objects and their progeny, methods etc.
species-method | AnnotationDb objects and their progeny, methods etc.
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
SYMBOL | Descriptions of available values for 'columns' and 'keytypes'.
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-method | Methods for manipulating a Bimap object in a data-frame style
TAIR | Descriptions of available values for 'columns' and 'keytypes'.
taxonomyId | AnnotationDb objects and their progeny, methods etc.
taxonomyId-method | AnnotationDb objects and their progeny, methods etc.
TERM | Descriptions of available values for 'columns' and 'keytypes' for GO.db.
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 --

UNIGENE | Descriptions of available values for 'columns' and 'keytypes'.
UNIPROT | Descriptions of available values for 'columns' and 'keytypes'.
unlist2 | A replacement for unlist() that does not mangle the names

## -- misc --

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