onto.GOCC: Gene Ontology Cellular Component (GOCC).

In dcGOR: Analysis of Ontologies and Protein Domain Annotations

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. Only the edges with the relation (either 'is_a' or 'part_of') are retained.

Usage

data(onto.GOCC)

Value

an object of S4 class Onto. It has slots for "nodeInfo" and "adjMatrix"

• nodeInfo: an object of S4 class InfoDataFrame, describing information on nodes/terms including: "term_id" (i.e. Term ID), "term_name" (i.e. Term Name), "term_namespace" (i.e. Term Namespace), and "term_distance" (i.e. Term Distance: the distance to the root; always 0 for the root itself)

• adjMatrix: an object of S4 class AdjData, containing adjacency data matrix, with rows for parent (arrow-outbound) and columns for children (arrow-inbound)

References

Ashburner et al. (2000) Gene ontology: tool for the unification of biology. Nat Genet, 25:25-29.
Fang H and Gough J. (2013) dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res, 41(Database issue):D536-44.

Examples

data(onto.GOCC)
onto.GOCC

Example output

Loading required package: Matrix
Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Loading required package: dnet
Loading required package: supraHex
Loading required package: hexbin

Attaching package: ‘dcGOR’

The following object is masked from ‘package:base’:

    write

An object of S4 class 'Onto'
@adjMatrix: a direct matrix of 3215 terms (parents/from) X 3215 terms (children/to) 
@nodeInfo (InfoDataFrame)
  nodeNames: GO:0005575 GO:0005576 GO:0005623 ... GO:0044192 GO:0044201
    (3215 total)
  nodeAttr: term_id term_name term_namespace term_distance

dcGOR documentation built on May 2, 2019, 3:34 p.m.