get_cl: Get Cell Ontology

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Get Cell Ontology

Description

A thin wrapper around get_ontology to get the specific version of the Cell Ontology used in the original analyses that produced the results stored in load_example_results.

Usage

get_cl(name = "cl", tag = "v2023-09-21", lvl = 1, remove_rings = TRUE, ...)

Arguments

name	<...>Any ontology name from get_ols_options "mondo" Import the Mondo ontology. GitHub.. "hpo" Import the Human Phenotype Ontology. GitHub.
tag	tag for the GitHub release to which this data should be attached.
lvl	Depth of the ancestor terms to add. Will get the closest ancestor to this level if none have this exact level.
remove_rings	Parameter passed to simona::import_ontology.
...	Arguments passed on to KGExplorer::get_ontology save_dir Directory to save a file to. force_new If TRUE, force a new download. method Compute ontology levels using: "height" (default) dag_height. "depth" dag_depth. filetype File type to search for. import_func Function to import the ontology with. If NULL, automatically tries to choose the correct function. terms A vector of ontology term IDs. add_metadata Add metadata to the resulting ontology object. add_n_edges Add the number of edges (connections) for each term. add_ontology_levels Add the ontology level for each term.

Examples

cl <- get_cl()

neurogenomics/MultiEWCE documentation built on April 17, 2025, 9:27 p.m.