# Calculating Ontological Similarities

## Documentation for package ‘ontologySimilarity’ version 2.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

ontologySimilarity-package | Functions for Calculating Ontological Similarities
create_sim_index | Create light-weight similarity index for fast lookups of between term set similarity.
descendants_IC | Get information content based on number of descendants each term has
gene_GO_terms | Gene Ontology annotation of genes
get_asym_sim_grid | Get asymmetrical similarity matrix
get_profile_sims | Get similarities of term sets to profile
get_sim | Calculate the group similarity of a set of row/column indices
get_sim.default | Calculate the group similarity of a set of row/column indices
get_sim.integer | Calculate the group similarity of a set of row/column indices
get_sim.matrix | Calculate the group similarity of a set of row/column indices
get_sim.numeric | Calculate the group similarity of a set of row/column indices
get_sim.sim_index | Calculate the group similarity of a set of row/column indices
get_similarity_rank_matrix | Get matrix of similarity rank from similarity matrix
get_sim_grid | Get similarity matrix of pairwise similarities of term sets.
get_sim_p | Get similarity p-value
get_sim_p.default | Get similarity p-value
get_sim_p.integer | Get similarity p-value
get_sim_p.matrix | Get similarity p-value
get_sim_p.numeric | Get similarity p-value
get_sim_p.sim_index | Get similarity p-value
get_sim_p_from_ontology | Get similarity p-value for subgroup of list of term sets
get_term_set_to_term_sims | Get 'term sets to term' similarity matrix
get_term_sim_mat | Get term-term similarity matrix
GO_IC | Gene Ontology terms information content.
lin | Calculate Lin similarity score of two term sets
ontologySimilarity | Functions for Calculating Ontological Similarities
resnik | Calculate Resnik similarity score of two term sets
sample_group_sim | Draw sample of group similarities of groups of given size
sample_group_sim.default | Draw sample of group similarities of groups of given size
sample_group_sim.integer | Draw sample of group similarities of groups of given size
sample_group_sim.matrix | Draw sample of group similarities of groups of given size
sample_group_sim.numeric | Draw sample of group similarities of groups of given size
sample_group_sim.sim_index | Draw sample of group similarities of groups of given size
sample_group_sim_from_ontology | Draw sample of group similarities for groups of given size based on 'ontology' argument