Gene Ontology Cellular Component (GOCC).

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 2017-03-27 19:58:54)
ig.GOCC
IGRAPH DN-- 3793 7116 -- + attr: name (v/c), term_id (v/c), term_name (v/c), term_distance | (v/n), relation (e/c) + edges (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