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/www.godatabase.org/dev
     /database/archive/latest/>. Built: 200504

     Package built: Tue May 17 09:56:06 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]
       }

