Annotation Database Interface


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Documentation for package ‘AnnotationDbi’ version 1.0.6

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

$,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-colmethods Methods for manipulating the col names of a Bimap object
Bimap-direction Methods for accessing/changing the direction of a Bimap object
Bimap-keymethods Methods for manipulating the keys of a Bimap object
Bimap-toTable Methods for extracting data from a Bimap object
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 the col names of a Bimap object
colmetanames,AnnDbBimap-method Methods for manipulating the col names of a Bimap object
colmetanames,FlatBimap-method Methods for manipulating the col names of a Bimap object
colnames Methods for manipulating the col names of a Bimap object
colnames,AnnDbBimap-method Methods for manipulating the col names of a Bimap object
colnames,FlatBimap-method Methods for manipulating the col names of a Bimap object
contents,Bimap-method Environment-like API for AnnDbBimap objects
count.links Methods for extracting data from a Bimap object
count.links,Bimap-method Methods for extracting data from a Bimap object
count.links,Go3AnnDbBimap-method Methods for extracting data from a Bimap object
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 manipulating the keys of a Bimap object
count.mappedLkeys,AgiAnnDbMap-method Methods for manipulating the keys of a Bimap object
count.mappedLkeys,AnnDbBimap-method Methods for manipulating the keys of a Bimap object
count.mappedLkeys,Bimap-method Methods for manipulating the keys of a Bimap object
count.mappedLkeys,Go3AnnDbBimap-method Methods for manipulating the keys of a Bimap object
count.mappedRkeys Methods for manipulating the keys of a Bimap object
count.mappedRkeys,AnnDbBimap-method Methods for manipulating the keys of a Bimap object
count.mappedRkeys,AnnDbMap-method Methods for manipulating the keys of a Bimap object
count.mappedRkeys,Bimap-method Methods for manipulating the keys of a Bimap object
count.mappedRkeys,Go3AnnDbBimap-method Methods for manipulating the keys of a Bimap object

-- 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 extracting data from a Bimap object
direction Methods for accessing/changing the direction of a Bimap object
direction,AnnDbBimap-method Methods for accessing/changing the direction of a Bimap object
direction,FlatBimap-method Methods for accessing/changing the direction of a Bimap object
direction<-,AnnDbBimap-method Methods for accessing/changing the direction of a Bimap object
direction<-,AnnDbMap-method Methods for accessing/changing the direction of a Bimap object
direction<-,FlatBimap-method Methods for accessing/changing the direction of a Bimap object

-- 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 extracting data from a Bimap object
head,FlatBimap-method Methods for extracting data from a Bimap object

-- 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 the col names of a Bimap object
keyname,Bimap-method Methods for manipulating the col names of a Bimap object
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 extracting data from a Bimap object
links,AnnDbBimap-method Methods for extracting data from a Bimap object
links,FlatBimap-method Methods for extracting data from a Bimap object
links,Go3AnnDbBimap-method Methods for extracting data from a Bimap object
Lkeyname Methods for manipulating the col names of a Bimap object
Lkeyname,AnnDbBimap-method Methods for manipulating the col names of a Bimap object
Lkeyname,Bimap-method Methods for manipulating the col names of a Bimap object
Lkeys Methods for manipulating the keys of a Bimap object
Lkeys,AnnDbBimap-method Methods for manipulating the keys of a Bimap object
Lkeys,FlatBimap-method Methods for manipulating the keys of a Bimap object
Lkeys<-,AnnDbBimap-method Methods for manipulating the keys of a Bimap object
Lkeys<-,FlatBimap-method Methods for manipulating the keys of a Bimap object
Llength Methods for manipulating the keys of a Bimap object
Llength,AnnDbBimap-method Methods for manipulating the keys of a Bimap object
Llength,Bimap-method Methods for manipulating the keys of a Bimap object
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
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 manipulating the keys of a Bimap object
mappedLkeys,AgiAnnDbMap-method Methods for manipulating the keys of a Bimap object
mappedLkeys,AnnDbBimap-method Methods for manipulating the keys of a Bimap object
mappedLkeys,FlatBimap-method Methods for manipulating the keys of a Bimap object
mappedLkeys,Go3AnnDbBimap-method Methods for manipulating the keys of a Bimap object
mappedRkeys Methods for manipulating the keys of a Bimap object
mappedRkeys,AnnDbBimap-method Methods for manipulating the keys of a Bimap object
mappedRkeys,AnnDbMap-method Methods for manipulating the keys of a Bimap object
mappedRkeys,FlatBimap-method Methods for manipulating the keys of a Bimap object
mappedRkeys,Go3AnnDbBimap-method Methods for manipulating the keys of a Bimap object
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 the col names of a Bimap object
ncol,Bimap-method Methods for manipulating the col names of a Bimap object
nhit Methods for extracting data from a Bimap object
nhit,Bimap-method Methods for extracting data from a Bimap object
nhit,environment-method Methods for extracting data from a Bimap object
nhit,list-method Methods for extracting data from a Bimap object
nrow Methods for extracting data from a Bimap object
nrow,AnnDbBimap-method Methods for extracting data from a Bimap object
nrow,AnnDbTable-method Methods for extracting data from a Bimap object
nrow,FlatBimap-method Methods for extracting data from a Bimap object
nrow,Go3AnnDbBimap-method Methods for extracting data from a Bimap object

-- O --

Ontology Class "GOTerms"
Ontology,GOTerms-method Class "GOTerms"

-- R --

Rattribnames Methods for manipulating the col names of a Bimap object
Rattribnames,AnnDbBimap-method Methods for manipulating the col names of a Bimap object
Rattribnames,Bimap-method Methods for manipulating the col names of a Bimap object
Rattribnames<-,AnnDbBimap-method Methods for manipulating the col names of a Bimap object
Rattribnames<-,FlatBimap-method Methods for manipulating the col names of a Bimap object
Rattribnames<-,Go3AnnDbBimap-method Methods for manipulating the col names of a Bimap object
revmap Methods for accessing/changing the direction of a Bimap object
revmap,AnnDbBimap-method Methods for accessing/changing the direction of a Bimap object
revmap,Bimap-method Methods for accessing/changing the direction of a Bimap object
revmap,environment-method Methods for accessing/changing the direction of a Bimap object
revmap,list-method Methods for accessing/changing the direction of a Bimap object
Rkeyname Methods for manipulating the col names of a Bimap object
Rkeyname,AnnDbBimap-method Methods for manipulating the col names of a Bimap object
Rkeyname,Bimap-method Methods for manipulating the col names of a Bimap object
Rkeys Methods for manipulating the keys of a Bimap object
Rkeys,AnnDbBimap-method Methods for manipulating the keys of a Bimap object
Rkeys,AnnDbMap-method Methods for manipulating the keys of a Bimap object
Rkeys,FlatBimap-method Methods for manipulating the keys of a Bimap object
Rkeys,Go3AnnDbBimap-method Methods for manipulating the keys of a Bimap object
Rkeys<-,AnnDbBimap-method Methods for manipulating the keys of a Bimap object
Rkeys<-,FlatBimap-method Methods for manipulating the keys of a Bimap object
Rlength Methods for manipulating the keys of a Bimap object
Rlength,AnnDbBimap-method Methods for manipulating the keys of a Bimap object
Rlength,AnnDbMap-method Methods for manipulating the keys of a Bimap object
Rlength,Bimap-method Methods for manipulating the keys of a Bimap object
Rlength,Go3AnnDbBimap-method Methods for manipulating the keys of a Bimap object

-- 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 manipulating the keys of a Bimap object
subset,AnnDbBimap-method Methods for manipulating the keys of a Bimap object
subset,Bimap-method Methods for manipulating the keys of a Bimap object
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 the col names of a Bimap object
tagname,AnnDbBimap-method Methods for manipulating the col names of a Bimap object
tagname,Bimap-method Methods for manipulating the col names of a Bimap object
tail Methods for extracting data from a Bimap object
tail,FlatBimap-method Methods for extracting data from a Bimap object
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 extracting data from a Bimap object
toTable,AnnDbBimap-method Methods for extracting data from a Bimap object
toTable,FlatBimap-method Methods for extracting data from a Bimap object

-- misc --

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