Description

An R object that contains information on UniProtKB UniPathway 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). UniProtKB UniPathway (UP) is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as a controlled vocabulary for pathway annotation in UniProtKB.

Usage

onto.UP <- dcRDataLoader(RData = "onto.UP")

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

Morgat et al. (2006) UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res, 40:D761-9.

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

onto.UP <- dcRDataLoader(RData='onto.UP')

'onto.UP' (from http://dcgor.r-forge.r-project.org/data/onto.UP.RData) has been loaded into the working environment
onto.UP

An object of S4 class 'Onto'
@adjMatrix: a direct matrix of 1039 terms (parents/from) X 1039 terms (children/to) 
@nodeInfo (InfoDataFrame)
  nodeNames: UPA00001 UPA00026 UPA00485 ... UPA01020 UPA00902 (1039
    total)
  nodeAttr: term_id term_name term_namespace term_distance