MICA_term               Various types of common ancestors
[,ontology_DAG,ANY,ANY,missing-method
                        Create sub-DAGs
add_annotation          Add annotations to the DAG object
all_term_IC_methods     Supported methods
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
dag_all_terms           Names of all terms
dag_as_igraph           Convert to an igraph object
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_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_has_terms           Whether the terms exist in the DAG
dag_longest_dist_to_offspring
                        Distance from all ancestors/to all offspring in
                        the DAG
dag_parents             Parent/child/ancestor/offspring terms
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_treelize            Reduce the DAG to a tree
group_sim               Semantic similarity between two groups of terms
import_obo              Import ontology file to an ontology_DAG object
mcols,ontology_DAG-method
                        Get or set meta columns on DAG
method_param            All Papameters of a given method
n_annotations           Number of annotated items
n_offspring             Number of parent/child/ancestor/offspring/leaf
                        terms
ontology_DAG-class      The ontology_DAG class
ontology_kw             Import ontologies already having gene
                        annotations
partition_by_level      Partition the DAG
print.print_source      Print the source
random_terms            Randomly sample terms/items
shortest_distances_via_NCA
                        Distance on the DAG
show,ontology_DAG-method
                        Print the ontology_DAG object
simona_opt              Global options
term_IC                 Information content
term_annotations        Term-item associations
term_sim                Semantic similarity
