get_ontology_db: Access an ontology database

In saezlab/OmnipathR: OmniPath web service client and more

Access an ontology database

Description

Retrieves an ontology database with relations in the desired data structure. The database is automatically loaded and the requested data structure is constructed if necessary. The databases stay loaded up to a certain time period (see the option omnipathr.db_lifetime). Hence the first one of repeated calls to this function might take long and the subsequent ones should be really quick.

Usage

get_ontology_db(key, rel_fmt = "tbl", child_parents = TRUE)

Arguments

key	Character: key of the ontology database. For the available keys see omnipath_show_db.
rel_fmt	Character: the data structure of the ontology relations. Posible values are 1) "tbl" a data frame, 2) "lst" a list or 3) "gra" a graph.
child_parents	Logical: whether the ontology relations should point from child to parents (TRUE) or from parent to children (FALSE).

Value

A list with the following elements: 1) "names" a table with term IDs and names; 2) "namespaces" a table to connect term IDs and namespaces they belong to; 3) "relations" a table with relations between terms and their parent terms; 4) "subsets" a table with terms and the subsets they are part of; 5) "obsolete" character vector with all the terms labeled as obsolete.

See Also

• omnipath_show_db

• get_db

Examples

go <- get_ontology_db('go_basic', child_parents = FALSE)

saezlab/OmnipathR documentation built on Oct. 16, 2024, 11:49 a.m.