get_ontology {ontologyIndex}

Read ontology from OBO file into R

Description

Read ontology from OBO file into R

Usage

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

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

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".

merge_equivalent_terms

Logical value determining whether terms that are marked "equivalent_to" a target term should be merged, retaining properties of the target term when the property should have one value, e.g. the term ID and name. Defaults to TRUE.

Value

ontology_index object.

See Also

get_relation_names