Description

An R object that contains information on Gene Ontology Cellular Component 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.GOCC <- dRDataLoader(RData = "ig.GOCC")

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

'ig.GOCC' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/ig.GOCC.RData?raw=true) has been loaded into the working environment (at 2018-01-19 12:37:06)
ig.GOCC

IGRAPH 6d9d513 DN-- 3793 7116 -- 
+ attr: name (v/c), term_id (v/c), term_name (v/c), term_distance
| (v/n), relation (e/c)
+ edges from 6d9d513 (vertex names):
 [1] GO:0000109->GO:0000110 GO:0000109->GO:0000111 GO:0000109->GO:0000112
 [4] GO:0000109->GO:0000113 GO:0000109->GO:0008622 GO:0000109->GO:0070312
 [7] GO:0000109->GO:0070522 GO:0000109->GO:0070912 GO:0000109->GO:0070913
[10] GO:0000109->GO:0071942 GO:0000112->GO:0000440 GO:0000118->GO:0016581
[13] GO:0000118->GO:0034967 GO:0000118->GO:0070210 GO:0000118->GO:0070211
[16] GO:0000118->GO:0070822 GO:0000118->GO:0070823 GO:0000118->GO:0070824
[19] GO:0000118->GO:1990483 GO:0000120->GO:0000500 GO:0000120->GO:0005668
+ ... omitted several edges