Annotation Database Interface

Documentation for package ‘AnnotationDbi’ version 1.16.19

DESCRIPTION file.
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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