GOMFANCESTOR               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 _t_o _t_h_e_i_r _M_o_l_e_c_u_l_a_r _F_u_n_c_t_i_o_n _A_n_c_e_s_t_o_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     This data set describes associations between GO molecular function
     (MF) terms and their ancestor MF terms, based on the directed
     acyclic graph (DAG) defined by the Gene Ontology Consortium. The
     format is an R environment mapping the GO MF terms to all ancestor
     terms, where an ancestor term is a more general GO term that
     precedes the given GO term in the DAG (in other words, the
     parents, and all their parents, etc.).

_D_e_t_a_i_l_s:

     Each GO MF term is mapped to a vector of ancestor GO MF terms.

     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:<URL:
     http://gopher5/compbio/annotationSourceData/archive.godatabase.org
     /latest/>. Built: 200509

     Package built: Fri Sep 30 02:51:32 2005

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.geneontology.org/> and <URL:
     http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene>

_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(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]
       }

