GOMFANCESTOR {GO}R Documentation

Annotation of GO identifiers by the GO identifiers of their ancestors

Description

This is an R environment (hash table) mapping GO ids to all the GO ids of their ancestors under molecular function (MF). Ancestors are defined as the direct or indirect parent/grand parent nodes of a given node for a GO id based on the directed acyclic graph defined by Gene Ontology Consortium. GO terms for ancestor nodes are more general

Details

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

Molecular function is defined as the tasks performed by individual gene products; examples are transcription factor and DNA helicase as defined by 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(GOMFANCESTOR)
  # Remove GO ids that do not have any ancestor
  xx <- xx[!is.na(xx)]
  if(length(xx) > 0){
    # Get the ancestor GO ids for the first two elents of xx
    goids <- xx[1:2]
  }

[Package GO version 1.6.5 Index]