ontologySimilarity-package |
Functions for Calculating Ontological Similarities |
create_sim_index |
Create similarity index for list of term sets |
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 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. |
group_term_enrichment |
Identify enriched terms in subgroup |
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 |
sample_group_sim.default |
Draw sample of group similarities |
sample_group_sim.integer |
Draw sample of group similarities |
sample_group_sim.matrix |
Draw sample of group similarities |
sample_group_sim.numeric |
Draw sample of group similarities |
sample_group_sim.sim_index |
Draw sample of group similarities |
sample_group_sim_from_ontology |
Draw sample of group similarities |