GOCCOFFSPRING {GO}R Documentation

Annotation of GO identifiers by the GO identifiers of their offspring

Description

This is an R environment (hash table) mapping GO ids to all the GO ids of their offspring under cellular component (CC). Offspring are defined as the direct or indirect children/grand children nodes of a given node for a GO id based on the directed acyclic graph defined by Gene Ontology Consortium. GO terms for offspring nodes are more specific

Details

GO ids are keys and the corresponding offspring GO ids are values. Values are vectors of GO ids for all the offspring of the key GO id. GO ids that do not have any offspring node are assigned NA as the values.

Cellular component is defined as the subcellular structures, locations, and macromolecular complexes; examples include nucleus, telomere, and origin recognition complex as defined b y Gene Ontology Consortium.

Mappings were based on data provided:

Gene Ontology:http://www.godatabase.org/dev/database/archive/2004-07-01/go_200407-termdb.xml.gz. Built: 2004-07-01

Package built: Tue Sep 28 11:27:36 2004

References

http://www.geneontology.org/ and http://www.ncbi.nlm.nih.gov/LocusLink

Examples

  require("GO", character.only = TRUE) || stop("GO unavailable")
  # Convert the environment object to a list
  xx <- as.list(GOCCOFFSPRING)
  # Remove GO ids that do not have any offspring
  xx <- xx[!is.na(xx)]
  if(length(xx) > 0){
    # Get the offspring GO ids for the first two elents of xx
    goids <- xx[1:2]
  }

[Package GO version 1.6.5 Index]