# Semantic Similarity on Bio-Ontologies

## Documentation for package ‘simona’ version 1.9.1

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

## Help Pages

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