Annotation Database Interface


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Documentation for package ‘AnnotationDbi’ version 1.4.3

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$,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