Semantic Similarity on Bio-Ontologies
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Documentation for package ‘simona’ version 1.7.1
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A C D G H I L M N O P R S T misc
-- A --
| add_annotation | Add annotations to the DAG object |
| all_group_sim_methods | Supported methods |
| all_term_IC_methods | Supported methods |
| all_term_sim_methods | Supported methods |
| alternative_GO_terms | Create the ontology_DAG object from the GO.db package |
| annotated_terms | Term-item associations |
| avg_children | Number of parent/child/ancestor/offspring/leaf terms |
| avg_parents | Number of parent/child/ancestor/offspring/leaf terms |
-- C --
| CA_terms | Various types of common ancestors |
| create_ontology_DAG | Create the ontology_DAG object |
| create_ontology_DAG_from_GO_db | Create the ontology_DAG object from the GO.db package |
| create_ontology_DAG_from_igraph | Create the ontology_DAG object from the igraph object |
-- D --
| dag_add_random_children | Generate a random DAG |
| dag_all_terms | Names of all terms |
| dag_ancestors | Parent/child/ancestor/offspring terms |
| dag_as_dendrogram | Reduce the DAG to a tree |
| dag_as_DOT | Visualize the DAG |
| dag_as_igraph | Convert to an igraph object |
| dag_children | Parent/child/ancestor/offspring terms |
| dag_circular_viz | Visualize the DAG |
| dag_depth | Depth and height in the DAG |
| dag_distinct_ancestors | Distinct ancestors of a list of terms |
| dag_enrich_on_genes | Enrichment analysis on the number of annotated items |
| dag_enrich_on_items | Enrichment analysis on the number of annotated items |
| dag_enrich_on_offsprings | Enrichment analysis on offspring terms |
| dag_enrich_on_offsprings_by_permutation | Enrichment analysis on offspring terms by permutation test |
| dag_filter | Filter the DAG |
| dag_graphviz | Visualize the DAG |
| dag_has_terms | Whether the terms exist in the DAG |
| dag_height | Depth and height in the DAG |
| dag_is_leaf | Root or leaves of the DAG |
| dag_leaves | Root or leaves of the DAG |
| dag_longest_dist_from_ancestors | Distance from all ancestors/to all offspring in the DAG |
| dag_longest_dist_to_offspring | Distance from all ancestors/to all offspring in the DAG |
| dag_n_leaves | Names of all terms |
| dag_n_relations | Names of all terms |
| dag_n_terms | Names of all terms |
| dag_offspring | Parent/child/ancestor/offspring terms |
| dag_parents | Parent/child/ancestor/offspring terms |
| dag_permutate_children | Reorder the DAG |
| dag_random | Generate a random DAG |
| dag_random_tree | Generate a random DAG |
| dag_reorder | Reorder the DAG |
| dag_root | Root or leaves of the DAG |
| dag_shiny | A shiny app for the DAG |
| dag_shortest_dist_from_ancestors | Distance from all ancestors/to all offspring in the DAG |
| dag_shortest_dist_from_root | Depth and height in the DAG |
| dag_shortest_dist_to_leaves | Depth and height in the DAG |
| dag_shortest_dist_to_offspring | Distance from all ancestors/to all offspring in the DAG |
| dag_siblings | Parent/child/ancestor/offspring terms |
| dag_treelize | Reduce the DAG to a tree |
-- G --
| group_sim | Semantic similarity between two groups of terms |
-- H --
| has_annotation | Number of annotated items |
-- I --
| import_obo | Import ontology file to an ontology_DAG object |
| import_ontology | Import ontology file to an ontology_DAG object |
| import_owl | Import ontology file to an ontology_DAG object |
| import_ttl | Import ontology file to an ontology_DAG object |
-- L --
| LCA_depth | Various types of common ancestors |
| LCA_term | Various types of common ancestors |
| longest_distances_directed | Distance on the DAG |
| longest_distances_via_LCA | Distance on the DAG |
-- M --
| max_ancestor_id | Various types of common ancestors |
| max_ancestor_path_sum | Various types of common ancestors |
| max_ancestor_v | Various types of common ancestors |
| mcols-method | Get or set meta columns on DAG |
| mcols<--method | Get or set meta columns on DAG |
| method_param | All Papameters of a given method |
| MICA_IC | Various types of common ancestors |
| MICA_term | Various types of common ancestors |
-- N --
| NCA_term | Various types of common ancestors |
| n_ancestors | Number of parent/child/ancestor/offspring/leaf terms |
| n_annotations | Number of annotated items |
| n_children | Number of parent/child/ancestor/offspring/leaf terms |
| n_connected_leaves | Number of parent/child/ancestor/offspring/leaf terms |
| n_offspring | Number of parent/child/ancestor/offspring/leaf terms |
| n_parents | Number of parent/child/ancestor/offspring/leaf terms |
-- O --
| ontology_chebi | Import ontologies already having gene annotations |
| ontology_DAG | The ontology_DAG class |
| ontology_DAG-class | The ontology_DAG class |
| ontology_go | Import ontologies already having gene annotations |
| ontology_hp | Import ontologies already having gene annotations |
| ontology_kw | Import ontologies already having gene annotations |
| ontology_pw | Import ontologies already having gene annotations |
| ontology_rdo | Import ontologies already having gene annotations |
| ontology_reactome | Import ontologies already having gene annotations |
| ontology_vt | Import ontologies already having gene annotations |
-- P --
| partition_by_level | Partition the DAG |
| partition_by_size | Partition the DAG |
| print.ontology_tree | Reduce the DAG to a tree |
| print.print_source | Print the source |
-- R --
| random_items | Randomly sample terms/items |
| random_terms | Randomly sample terms/items |
-- S --
| shortest_distances_directed | Distance on the DAG |
| shortest_distances_via_NCA | Distance on the DAG |
| show-method | Print the ontology_DAG object |
| simona_opt | Global options |
-- T --
| term_annotations | Term-item associations |
| term_IC | Information content |
| term_sim | Semantic similarity |
-- misc --
| [-method | Create sub-DAGs |
| [[-method | Create sub-DAGs |