Gene Ontology Molecular Function (GOMF).

Description

An R object that contains information on Gene Ontology Molecular Function terms. These terms are organised as a direct acyclic graph (DAG), which is further stored as an object of the class 'igraph' (see http://igraph.org/r/doc/aaa-igraph-package.html). This data is prepared based on http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo.

Usage

ig.GOMF <- dRDataLoader(RData = "ig.GOMF")

Value

an object of class "igraph". As a direct graph, it has attributes to vertices/nodes and edges:

  • vertex attributes: "name" (i.e. "Term ID"), "term_id" (i.e. "Term ID"), "term_name" (i.e "Term Name") and "term_distance" (i.e. Term Distance: the distance to the root; always 0 for the root itself)
  • edge attributes: "relation" (either 'is_a' or 'part_of')

References

Ashburner et al. (2000) Gene ontology: tool for the unification of biology. Nat Genet, 25:25-29.

Examples

ig.GOMF <- dRDataLoader(RData='ig.GOMF')
'ig.GOMF' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/ig.GOMF.RData?raw=true) has been loaded into the working environment (at 2017-03-27 19:58:58)
ig.GOMF
IGRAPH DN-- 9933 12114 -- + attr: name (v/c), term_id (v/c), term_name (v/c), term_distance | (v/n), relation (e/c) + edges (vertex names): [1] GO:0000009->GO:0033164 GO:0000009->GO:0052824 GO:0000009->GO:0052917 [4] GO:0000014->GO:1990599 GO:0000014->GO:1990601 GO:0000026->GO:0004377 [7] GO:0000026->GO:0052918 GO:0000026->GO:0052926 GO:0000030->GO:0000009 [10] GO:0000030->GO:0000026 GO:0000030->GO:0000033 GO:0000030->GO:0004169 [13] GO:0000030->GO:0004376 GO:0000030->GO:0004582 GO:0000030->GO:0004584 [16] GO:0000030->GO:0016438 GO:0000030->GO:0019187 GO:0000030->GO:0047252 [19] GO:0000030->GO:0047264 GO:0000030->GO:0047267 GO:0000030->GO:0051751 + ... omitted several edges