Manipulation of SQLite-based annotations in Bioconductor

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Documentation for package ‘AnnotationDbi’ version 1.56.2

• 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