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:

     GOCCPARENTS mappes 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:

     This is an environment object with key and value pairs. 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 Consortium built: 2004-02-01.<URL:
     http://www.godatabase.org/dev/database/archive/2004-02-01/go_20040
     2-termdb.xml.gz>

     Package built: Wed Mar  3 16:27:29 2004

_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")
       # 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){
          # Get the first element
          xx[[1]]
          # Get more than one elements
          xx[1:3]
          goids <- xx[[1]]
       }

