get_ontology: Read ontology from OBO file into R

Description Usage Arguments Value See Also

View source: R/data.R

Description

Read ontology from OBO file into R

Usage

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get_ontology(file, propagate_relationships = "is_a", extract_tags = "minimal")

get_OBO(file, propagate_relationships = "is_a", extract_tags = "minimal")

Arguments

file

File path of OBO formatted file.

propagate_relationships

Character vector of relations

extract_tags

Character value: either "minimal" or "everything", determining whether to extract only the properties of terms which are required to run functions in the package - i.e. "id", "name", "parents", "children" and "ancestors" - or extract all properties provided in the file. Term properties are named in the resulting ontology_index as their corresponding tags in the OBO file (except "parents", "children" and "ancestors" which are appended with "_OBO" to avoid clashing with standard ontology_index properties. Defaults to "minimal".

Value

ontology_index object.

See Also

get_relation_names


ontologyIndex documentation built on Feb. 4, 2021, 1:06 a.m.