Toolbox for bio-ontology analysis.

Basic

Example

library(simona)
dag = create_ontology_DAG_from_GO_db("BP", org_db = "org.Hs.eg.db")
dag

## An ontology_DAG object:
##   Source: GO BP / GO.db package 3.20.0 
##   26552 terms / 51745 relations
##   Root: GO:0008150 
##   Terms: GO:0000001, GO:0000002, GO:0000011, GO:0000012, ...
##   Max depth: 18 
##   Avg number of parents: 1.95
##   Avg number of children: 1.83
##   Aspect ratio: 343.15:1 (based on the longest distance from root)
##                 756.89:1 (based on the shortest distance from root)
##   Relations: is_a, part_of
##   Annotations: 18986 items
##                291, 1890, 4205, 4358, ...
## 
## With the following columns in the metadata data frame:
##   id, name, definition