In much the same way as an
AnnotationDb object allows access to
select for many other annotation packages,
PANTHER.db is meant
to allow usage of
select methods and other supporting methods
to enable the easy extraction of data from the PANTHER gene ontology.
keys are used together to
extract data via an
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 via the
keys returns keys for the database contained in the
PANTHER.db object. By default it will return the primary keys
for the database, which are FAMILY_ID keys, 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
pthOrganisms shows the organism label currently attached to
PANTHER.db objects database. The organism supported by
PANTHER.db is currently restricted to the organisms supported by
the main annotation packages in Bioconductor.
PANTHER.db object will be loaded whenever you load the
PANTHER.db package. This object will be set up to return
information on PANTHER ontology terms and accessions based on
all available organisms. The
pthOrganisms<- method can be used
to restrict queries to a specific organism and
can be used to remove the organism restriction.
availablePthOrganisms is a helper function to list out the
available Species currently supported by the
along with their official taxonomy IDs that are available by Uniprot.
The PANTHER Protein Class ontology was adapted from the PANTHER/X
molecular function ontology, and includes commonly used classes of
protein functions, many of which are not covered by GO molecular function.
traverseClassTree can be used to traverse the tree structure of
the PANTHER Protein Class ontology.
1 2 3 4 5 6 7 8
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
the keytype that matches the keys used. For the
character vector of valid PANTHER class identifiers e.g.
each return a character vector of possible values.
availablePthOrganisms each return a data.frame.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
## look at the object PANTHER.db ## get the current organism pthOrganisms(PANTHER.db) ## list the possible key types keytypes(PANTHER.db) ## list the columns that can be retreived columns(PANTHER.db) ## list all possible keys of type entrez gene ID. head(keys(PANTHER.db)) ## use select to extract some data keys <- c("E1C9F4","O14618") cols <- c("FAMILY_ID","SPECIES","FAMILY_TERM") kt <- "UNIPROT" select(PANTHER.db, keys, cols, kt)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.