create_sim_index {ontologySimilarity}

Create similarity index for list of term sets

Description

Create light-weight similarity index for fast lookups of between term set similarity.

Usage

create_sim_index(
  ontology,
  term_sets,
  information_content = descendants_IC(ontology),
  term_sim_method = "lin",
  combine = "average"
)

Arguments

ontology

ontology_index object.

term_sets

List of character vectors of ontological term IDs.

information_content

Numeric vector of information contents of terms (named by term)

term_sim_method

Character string equalling either "lin" or "resnik" to use Lin or Resnik's expression for the similarity of terms.

combine

Character string - either "average" or "product", indicating whether to use the best-match-product' method, or function accepting two arguments - the first, the similarity matrix obtained by averaging across term sets in term_sets, and the second averaging across those in term_sets2.

Value

Object of class sim_index.

See Also

link{get_sim} get_sim_p sample_group_sim