create_sim_index: Create similarity index for list of term sets

In ontologySimilarity: Calculating Ontological Similarities

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

ontologySimilarity documentation built on May 29, 2024, 3:51 a.m.