Calculate the Resnik or Lin semantic similarity — calculate_semantic

This function calculates the semantic similarities based on Resnik or Lin similarity for a given ontology. Has also the option to calculate a combined version of the two.

Usage

calculate_semantic_sim(
  terms,
  similarity_type,
  ancestor_list,
  ic_list,
  add_self = FALSE
)

Arguments

terms: Vector of strings. The terms in the ontology you wish to screen.
similarity_type: String. One of c("resnik", "lin", "combined").
ancestor_list: List. Names being the term and the elements in the list the names of the ancestors, see get_ontology_ancestry().
ic_list: List. The names being the term and the elements the information content of this given term. Needs to be a single float! See calculate_information_content().
add_self: Boolean. Shall self-similarities be added. Defaults to FALSE.

Value

A data.table with the calculated similarities.