Functions for Reading Ontologies into R


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Documentation for package ‘ontologyIndex’ version 2.0

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ontologyIndex-package Functions for Reading Ontologies into R
exclude_branches Exclude terms descending from particular term from a character vector of terms
force_compatibility Remove alternate/deprecated term IDs and swap for new ones
get_ancestors Get set of all ancestors of set of terms
get_descendants Get set of all descendants of single term
get_mpo_to_hpo Get MPO to HPO list
get_ontology Get R-Object representation of ontology from obo file
get_terms_by_set_matrix Get a matrix with columns of hpo terms and rows of patients,
get_term_ancestors Get property of individual ontological term
get_term_children Get property of individual ontological term
get_term_descendancy_matrix Get logical descendancy matrix for set of terms
get_term_frequencies Get frequency of each term in a set of phenotypes
get_term_info_content Get information content of each term in a set of phenotypes
get_term_names Get property of individual ontological term
get_term_parents Get property of individual ontological term
get_term_property Get property of individual ontological term
go GO index
hpo HPO index
intersection_with_branches Intersect set of terms with branches of ontology
minimal_set Remove redundant/implied terms
mpo MPO index
mpo_to_hpo Mapping from MPO to HPO
ontologyIndex Functions for Reading Ontologies into R
prune_branches Prune all terms descending from given term down to that term and ensure no degeneracy