GOCCPARENTS                package:GO                R Documentation

_A_n_n_o_t_a_t_i_o_n _o_f _G_O _i_d_e_n_t_i_f_i_e_r_s _b_y _t_h_e _G_O _i_d_e_n_t_i_f_i_e_r_s _o_f _t_h_e_i_r
_d_i_r_e_c_t _p_a_r_e_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     This is an R environment (hash table) mapping GO ids to the GO ids
     of their direct parents under cellular component (CC). Direct
     parents of a given GO id are those GO ids correponding to all the
     parents nodes that have direct link to the node for the GO id of
     concern based on the directed acyclic graph defined by Gene
     Ontology Consortium. GO terms for parent nodes are more general
     than that of the child nods

_D_e_t_a_i_l_s:

     GO ids are keys and the corresponding parent GO ids are values.
     Values are named vectors of length 1 or greater depending on
     whether the GO id of concern has only one or more parents. The
     name(s) of value(s) is(are) the association code (isa or partof)
     between the GO id and its direct parents.GO ids that do not have
     any parent 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:<URL:
     http://www.godatabase.org/dev/database/archive/2004-09-01/go_20040
     9-termdb.xml.gz>. Built: 2004-09-01

     Package built: Mon Jan 10 19:19:56 2005

_R_e_f_e_r_e_n_c_e_s:

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

_E_x_a_m_p_l_e_s:

       require("GO", character.only = TRUE) || stop("GO unavailable")
       require("annotate", character.only = TRUE) || stop("annoate unavailable")
       # Convert the environment object to a list
       xx <- as.list(GOCCPARENTS)
       # Remove GO ids that do not have any parent
       xx <- xx[!is.na(xx)]
       if(length(xx) > 0){
          goids <- xx[[1]]
          # Find out the GO terms for the first parent goid
          GOID(GOTERM[[goids[1]]])
          Term(GOTERM[[goids[1]]])
          Synonym(GOTERM[[goids[1]]])
          Secondary(GOTERM[[goids[1]]])
          Definition(GOTERM[[goids[1]]])
       }

