hgu95av2GO             package:hgu95av2             R Documentation

_A_n_n_o_t_a_t_i_o_n _o_f _p_r_o_b_e _i_d_s _b_y _G_e_n_e _O_n_t_o_l_o_g_y _i_n_f_o_r_m_a_t_i_o_n

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

     hgu95av2GO mappes probe ids to Gene Ontology information including
     GO ids, evidence codes, and GO categories based on data collected
     from LocusLink and Gene Ontology consortium for the genes
     represented by the probe ids.

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

     This is an environment object with key and value pairs. Keys are
     probe ids and values are lists containing one (mapped to none or
     one set of GO information) or more (mapped to more than one sets
     of GO information) elements. When a probe id is mapped to at lest
     one set of GO information, each element of the list contains a sub
     list of three elements named "GOID", "Ontology", and "Evidence".
     Values for element "GOID" gives the Gene Ontology identifiers the
     key probe ids corresponding to. Values for element "Ontology" can
     be an abbreviation of MF (mocular function), BP (biological
     process), or CC (cellular component) for the GO category the GO id
     belongs to. Values for element "Evidence" contain an evidence code
     indicating what kind of evidence is found to support the
     association of the GO id to the key probe id. The evidence codes
     in use include:

     IMP: inferred from mutant phenotype   IGI: inferred from genetic
     interaction IPI: inferred from physical interaction   ISS:
     inferred from sequence similarity  IDA: inferred from direct assay
       IEP: inferred from expression pattern   IEA: inferred from
     electronic annotation   TAS: traceable author statement   NAS:
     non-traceable author statement   ND: no biological data available 
      IC: inferred by curator

     Mappings between probe ids and GO information were obtained
     through their mappings to LocusLink ids. NA is assigned to probe
     identifiers that can not be mapped to any Gene Ontology
     information. Mappings between Gene Ontology ids an Gene Ontology
     terms and other information are available in a separate data
     package named GO.

     Mappings were based on data provided by:

     LocusLink built: March  3, 2004. <URL:
     ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.ga>

     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: ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz>

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

         # Convert to a list
         xx <- as.list(hgu95av2GO)
         # Remove all the NAs
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
                 # Try the firest one
                 got <- xx[[1]]           
                 got[[1]][["GOID"]]
                 got[[1]][["Ontology"]]
                 got[[1]][["Evidence"]]

         }

