GOMFPARENTS                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 Molecular function (MF). 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. 

     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 by:

     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(GOMFPARENTS)
         # Remove GO ids that do not have any parent
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
             # Get the parent GO ids for the first elents of xx
             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]]])
         }

