Description

An R object that contains information on Gene Ontology Biological Process 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.GOBP <- dRDataLoader(RData = "ig.GOBP")

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.GOBP <- dRDataLoader(RData='ig.GOBP')

'ig.GOBP' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/ig.GOBP.RData?raw=true) has been loaded into the working environment (at 2018-01-19 12:37:04)
ig.GOBP

IGRAPH ecbf51a DN-- 27685 58979 -- 
+ attr: name (v/c), term_id (v/c), term_name (v/c), term_distance
| (v/n), relation (e/c)
+ edges from ecbf51a (vertex names):
 [1] GO:0000002->GO:0032042 GO:0000002->GO:0033955 GO:0000003->GO:0019953
 [4] GO:0000003->GO:0019954 GO:0000003->GO:0032504 GO:0000003->GO:0032505
 [7] GO:0000003->GO:0051321 GO:0000012->GO:1903823 GO:0000012->GO:1990396
[10] GO:0000018->GO:0000019 GO:0000018->GO:0000337 GO:0000018->GO:0010520
[13] GO:0000018->GO:0010569 GO:0000018->GO:0045191 GO:0000018->GO:0045910
[16] GO:0000018->GO:0045911 GO:0000018->GO:0060542 GO:0000018->GO:0072695
[19] GO:0000018->GO:1903110 GO:0000019->GO:0032207 GO:0000019->GO:0045950
+ ... omitted several edges