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