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Calculate the semantic similarity in an ontology

rs_onto_semantic_sim_mat.Rd

This function calculates the specified semantic similarity and returns the full vector (only calculating the upper triangle) for the given similarity.

Usage

rs_onto_semantic_sim_mat(sim_type, ancestor_list, ic_list, flat_matrix)

Arguments

sim_type

String. Must be one of c("resnik", "lin", "combined").

ancestor_list

R list with names being the term and the elements in the list the names of the ancestors.

ic_list

R list with the names being the term and the elements the information content of this given term. Needs to be a single float!

flat_matrix

Boolean. Shall only the upper triangle be returned.

Value

A list with:

  • sim_mat - the semantic similarity matrix (flat or as matrix.)

  • names - the row and column names for the calculated matrix.