agGO                   package:ag                   R Documentation

_M_a_p _b_e_t_w_e_e_n _M_a_n_u_f_a_c_t_u_r_e_r _I_D_s _a_n_d _G_e_n_e _O_n_t_o_l_o_g_y (_G_O)

_D_e_s_c_r_i_p_t_i_o_n:

     agGO is an R environment that provides mappings between
     manufacturer ids and GO ids.

_D_e_t_a_i_l_s:

     Each manufacturer id is mapped to a named vector of GO ids. The
     name associated with each GO id corresponds to the evidence code
     for that GO id. Evidence codes currently 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 Entrez Gene ids. NAs are 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:

     Entrez Gene:<URL:
     http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/g
     ene/DATA/>. Built: Source data downloaded from Entrez Gene on Tue
     May 17 18:26:20 2005

     Gene Ontology:<URL:
     http://gopher5/compbio/annotationSourceData/www.godatabase.org/dev
     /database/archive/latest//go_200504-termdb.rdf-xml.gz>. Built:
     200504

     Package built Tue May 17 18:29:49 2005

_E_x_a_m_p_l_e_s:

         # Convert to a list
         xx <- as.list(agGO)
         # 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"]]

         }

