Function reference • simona

All functions
`add_annotation()`	Add annotations to the DAG object
`all_term_IC_methods()` `all_term_sim_methods()` `all_group_sim_methods()`	Supported methods
`term_annotations()` `annotated_terms()`	Term-item associations
`MICA_term()` `MICA_IC()` `LCA_term()` `LCA_depth()` `NCA_term()` `max_ancestor_v()` `max_ancestor_id()` `max_ancestor_path_sum()` `CA_terms()`	Various types of common ancestors
`create_ontology_DAG()`	Create the ontology_DAG object
`create_ontology_DAG_from_GO_db()` `alternative_GO_terms()`	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()` `dag_n_terms()` `dag_n_relations()` `dag_n_leaves()`	Names of all terms
`dag_as_igraph()`	Convert to an igraph object
`dag_depth()` `dag_height()` `dag_shortest_dist_from_root()` `dag_shortest_dist_to_leaves()`	Depth and height in the DAG
`dag_distinct_ancestors()`	Distinct ancestors of a list of terms
`dag_enrich_on_items()` `dag_enrich_on_genes()`	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()` `dag_shortest_dist_to_offspring()` `dag_longest_dist_from_ancestors()` `dag_shortest_dist_from_ancestors()`	Distance from all ancestors/to all offspring in the DAG
`dag_random_tree()` `dag_add_random_children()` `dag_random()`	Generate a random DAG
`dag_reorder()` `dag_permutate_children()`	Reorder the DAG
`dag_root()` `dag_leaves()` `dag_is_leaf()`	Root or leaves of the DAG
`dag_shiny()`	A shiny app for the DAG
`dag_parents()` `dag_children()` `dag_siblings()` `dag_ancestors()` `dag_offspring()`	Parent/child/ancestor/offspring terms
`dag_treelize()` `dag_as_dendrogram()` `print(<ontology_tree>)`	Reduce the DAG to a tree
`dag_circular_viz()` `dag_as_DOT()` `dag_graphviz()`	Visualize the DAG
`shortest_distances_via_NCA()` `longest_distances_via_LCA()` `shortest_distances_directed()` `longest_distances_directed()`	Distance on the DAG
`group_sim()`	Semantic similarity between two groups of terms
`import_obo()` `import_owl()` `import_ontology()` `import_ttl()`	Import ontology file to an ontology_DAG object
`mcols(<ontology_DAG>)` `mcols<-`(<ontology_DAG>)	Get or set meta columns on DAG
`method_param()`	All Papameters of a given method
`n_annotations()` `has_annotation()`	Number of annotated items
`n_offspring()` `n_ancestors()` `n_connected_leaves()` `n_parents()` `n_children()` `avg_parents()` `avg_children()`	Number of parent/child/ancestor/offspring/leaf terms
`ontology_kw()` `ontology_chebi()` `ontology_hp()` `ontology_pw()` `ontology_rdo()` `ontology_vt()` `ontology_go()`	Import ontologies already having gene annotations
`ontology_DAG-class` `ontology_DAG`	The ontology_DAG class
`partition_by_level()` `partition_by_size()`	Partition the DAG
`print(<print_source>)`	Print the source
`random_terms()` `random_items()`	Randomly sample terms/items
`show(<ontology_DAG>)`	Print the ontology_DAG object
`simona_opt()`	Global options
`[`(<ontology_DAG>,<ANY>,<ANY>,<missing>) `[`(<ontology_DAG>,<ANY>,<ANY>,<ANY>) `[`(<ontology_DAG>,<ANY>,<missing>,<missing>) `[`(<ontology_DAG>,<ANY>,<missing>,<ANY>) `[`(<ontology_DAG>,<missing>,<ANY>,<missing>) `[`(<ontology_DAG>,<missing>,<ANY>,<ANY>) `[`(<ontology_DAG>,<missing>,<missing>,<missing>) `[`(<ontology_DAG>,<missing>,<missing>,<ANY>) `[[`(<ontology_DAG>,<character>,<missing>)	Create sub-DAGs
`GroupSim_Dice()`	GroupSim_Dice
`GroupSim_Jaccard()`	GroupSim_Jaccard
`GroupSim_Kappa()`	GroupSim_Kappa
`GroupSim_Overlap()`	GroupSim_Overlap
`GroupSim_SimALD()`	GroupSim_SimALD
`GroupSim_SimALN()`	GroupSim_SimALN
`GroupSim_SimCHO()`	GroupSim_SimCHO
`GroupSim_SimCOT()`	GroupSim_SimCOT
`GroupSim_SimCOU()`	GroupSim_SimCOU
`GroupSim_SimDB()`	GroupSim_SimDB
`GroupSim_SimDIC()`	GroupSim_SimDIC
`GroupSim_SimGIC()`	GroupSim_SimGIC
`GroupSim_SimLP()`	GroupSim_SimLP
`GroupSim_SimNTO()`	GroupSim_SimNTO
`GroupSim_SimUB()`	GroupSim_SimUB
`GroupSim_SimUI()`	GroupSim_SimUI
`GroupSim_SimUIC()`	GroupSim_SimUIC
`GroupSim_Ye_2005()`	GroupSim_Ye_2005
`GroupSim_pairwise_ABM()`	GroupSim_pairwise_ABM
`GroupSim_pairwise_BMA()`	GroupSim_pairwise_BMA
`GroupSim_pairwise_BMM()`	GroupSim_pairwise_BMM
`GroupSim_pairwise_Froehlich_2007()`	GroupSim_pairwise_Froehlich_2007
`GroupSim_pairwise_HDF()`	GroupSim_pairwise_HDF
`GroupSim_pairwise_Joeng_2014()`	GroupSim_pairwise_Joeng_2014
`GroupSim_pairwise_MHDF()`	GroupSim_pairwise_MHDF
`GroupSim_pairwise_VHDF()`	GroupSim_pairwise_VHDF
`GroupSim_pairwise_avg()`	GroupSim_pairwise_avg
`GroupSim_pairwise_max()`	GroupSim_pairwise_max
`IC_Meng_2012()`	IC_Meng_2012
`IC_Sanchez_2011()`	IC_Sanchez_2011
`IC_Seco_2004()`	IC_Seco_2004
`IC_Seddiqui_2010()`	IC_Seddiqui_2010
`IC_Wang_2007()`	IC_Wang_2007
`IC_Zhang_2006()`	IC_Zhang_2006
`IC_Zhou_2008()`	IC_Zhou_2008
`IC_annotation()`	IC_annotation
`IC_height()`	IC_depth
`IC_offspring()`	IC_offspring
`IC_universal()`	IC_universal
`Sim_AIC_2014()`	Sim_AIC_2014
`Sim_AlMubaid_2006()`	Sim_AlMubaid_2006
`Sim_Ancestor()`	Sim_Ancestor
`Sim_Dice()`	Sim_Dice
`Sim_EISI_2015()`	Sim_EISI_2015
`Sim_FaITH_2010()`	Sim_FaITH_2010
`Sim_GOGO_2018()`	Sim_GOGO_2018
`Sim_HRSS_2013()`	Sim_HRSS_2013
`Sim_Jaccard()`	Sim_Jaccard
`Sim_Jiang_1997()`	Sim_Jiang_1997
`Sim_Kappa()`	Sim_Kappa
`Sim_Leocock_1998()`	Sim_Leocock_1998
`Sim_Li_2003()`	Sim_Li_2003
`Sim_Lin_1998()`	Sim_Lin_1998
`Sim_Overlap()`	Sim_Overlap
`Sim_Pekar_2002()`	Sim_Pekar_2002
`Sim_RSS_2013()`	Sim_RSS_2013
`Sim_Rada_1989()`	Sim_Rada_1989
`Sim_Relevance_2006()`	Sim_Relevance_2006
`Sim_Resnik_1999()`	Sim_Resnik_1999
`Sim_Resnik_edge_2005()`	Sim_Resnik_edge_2005
`Sim_SSDD_2013()`	Sim_SSDD_2013
`Sim_Shen_2010()`	Sim_Shen_2010
`Sim_Shenoy_2012()`	Sim_Shenoy_2012
`Sim_SimIC_2010()`	Sim_SimIC_2010
`Sim_Slimani_2006()`	Sim_Slimani_2006
`Sim_Stojanovic_2001()`	Sim_Stojanovic_2001
`Sim_WP_1994()`	Sim_WP_1994
`Sim_Wang_2007()`	Sim_Wang_2007
`Sim_Wang_edge_2012()`	Sim_Wang_edge_2012
`Sim_XGraSM_2013()`	Sim_XGraSM_2013
`Sim_Zhang_2006()`	Sim_Zhang_2006
`Sim_Zhong_2002()`	Sim_Zhong_2002
`Sim_universal()`	Sim_universal
`term_IC()`	Information content
`term_sim()`	Semantic similarity

Reference

All functions