AnnotationDb objects and their progeny, methods etc.
AnnotationDb is the virtual base class for all annotation
packages. It contain a database connection and is meant to be the
parent for a set of classes in the Bioconductor annotation
packages. These classes will provide a means of dispatch for a
widely available set of
select methods and thus allow the
easy extraction of data from the annotation packages.
keys are used together to
extract data from an
AnnotationDb object (or any object derived
from the parent class). Examples of classes derived from the
AnnotationDb object include (but are not limited to):
columns shows which kinds of data can be returned for the
keytypes allows the user to discover which keytypes can be
passed in to
keys and the
keys returns keys for the database contained in the
AnnotationDb object . This method is already documented in the
keys manual page but is mentioned again here because it's usage with
select is so intimate. By default it will return the primary
keys for the database, but if used with the
it will return the keys from that keytype.
select will retrieve the data as a data.frame based on
parameters for selected
saveDb will take an AnnotationDb object and save the database
to the file specified by the path passed in to the
loadDb takes a .sqlite database file as an argument and uses
data in the metadata table of that file to return an AnnotationDb
style object of the appropriate type.
species shows the genus and species label currently attached to
AnnotationDb objects database.
columns(x) keytypes(x) keys(x, keytype, ...) select(x, keys, columns, keytype, ...) saveDb(x, file) loadDb(file, dbType, dbPackage, ...)
AnnotationDbobject. But in practice this will mean an object derived from an
AnnotationDbobject such as a
- the keys to select records for from the database. All possible
keys are returned by using the
- the columns or kinds of things that can be retrieved
from the database. As with
keys, all possible columns are returned by using the
- the keytype that matches the keys used. For the
selectmethods, this is used to indicate the kind of ID being used with the keys argument. For the
keysmethod this is used to indicate which kind of keys are desired from
sqlitefile path. A string the represents the full name you want for your sqlite database and also where to put it.
- dbType - not required
- dbPackage - not required
- other arguments. These include:
- the pattern to match (used by keys)
- the column to search on. This is used by keys and is for when the thing you want to pattern match is different from the keytype, or when you want to simply want to get keys that have a value for the thing specified by the column argument.
- TRUE or FALSE value. Use fuzzy matching? (this is used with pattern by the keys method)
keytypeseach return a character vector or possible values.
selectreturns a data.frame.
require(hgu95av2.db) ## display the columns columns(hgu95av2.db) ## get the 1st 6 possible keys keys <- head( keys(hgu95av2.db) ) keys ## lookup gene symbol and unigene ID for the 1st 6 keys select(hgu95av2.db, keys=keys, columns = c("SYMBOL","UNIGENE")) ## get keys based on unigene keyunis <- head( keys(hgu95av2.db, keytype="UNIGENE") ) keyunis ## list supported key types keytypes(hgu95av2.db) ## lookup gene symbol and unigene ID based on unigene IDs by setting ## the keytype to "UNIGENE" and passing in unigene keys: select(hgu95av2.db, keys=keyunis, columns = c("SYMBOL","UNIGENE"), keytype="UNIGENE")