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
arguments. Users should be warned that if you call
select and request
columns that have multiple matches for your keys, select will return a
data.frame with one row for each possible match. This has the effect that if
you request multiple columns and some of them have a many to one relationship
to the keys, things will continue to multiply accordingly. So it's not a good
idea to request a large number of columns unless you know that what you are
asking for should have a one to one relationship with the initial set of keys.
In general, if you need to retrieve a column (like GO) that has a many to one
relationship to the original keys, it is most useful to extract that
mapIds gets the mapped ids (column) for a set of keys that are of a
particular keytype. Usually returned as a named character vector.
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.
dbfile gets the database file associated with an object.
dbconn gets the datebase connection associated with an object.
taxonomyId gets the taxonomy ID associated with an object (if available).