Calculating Ontological Similarities
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Documentation for package ‘ontologySimilarity’ version 2.7
Help Pages
| 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 |