Skip to contents

Load a GO sub-ontology graph from GO.db

Source: R/load_go.R
load_go.Rd

Loads a single Gene Ontology (GO) sub-ontology (BP, MF, or CC) from the Bioconductor annotation package GO.db and constructs an in-memory directed acyclic graph (DAG) representation.

The returned GO object contains GO term metadata together with the parent–child relationships required for graph traversal and downstream restriction operations. The ontology snapshot corresponds to the installed version of GO.db, which is recorded in the returned object for reproducibility.

Usage

load_go(ont = c("BP", "MF", "CC"), include_obsolete = FALSE, version = NULL)

Arguments

ont

character(1) GO sub-ontology to load. One of "BP", "MF", or "CC".

include_obsolete

logical(1) Whether obsolete GO terms should be included. If FALSE (default), obsolete terms are removed from the graph.

version

Optional character(1) specifying the expected GO.db version. If provided, the installed version must match.

Value

A GO S4 object representing the requested GO sub-ontology. The object contains:

  • GO term metadata

  • parent–child relationships defining the ontology DAG

  • adjacency lists for efficient graph traversal

  • an empty GO-to-gene mapping table to be populated with attach_org()

  • the GO.db version used to construct the graph

Details

The ontology graph loaded by load_go() serves as the starting point for GO restriction workflows implemented in this package. Organism-specific mappings can be attached using attach_org(), and the graph can subsequently be restricted using functions such as filter_mapped() or subset_go().

Examples

go_cc <- load_go("CC")
#> 
class(go_cc)
#> [1] "GO"
#> attr(,"package")
#> [1] "GOcontext"