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. select
, columns
and 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):
ChipDb
, OrgDb
GODb
, InparanoidDb
and
ReactomeDb
.
columns
shows which kinds of data can be returned for the
AnnotationDb
object.
keytypes
allows the user to discover which keytypes can be
passed in to select
or keys
and the keytype
argument.
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 keytype
argument,
it will return the keys from that keytype.
select
will retrieve the data as a data.frame based on
parameters for selected keys
and columns
and keytype
arguments.
saveDb
will take an AnnotationDb object and save the database
to the file specified by the path passed in to the file
argument.
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
the AnnotationDb
objects database.