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 identifiers and the GO identifiers that they are 
     directly associated with.

_D_e_t_a_i_l_s:

     Each Entrez Gene identifier is mapped to a list of lists.  The
     names on the outer list are GO identifiers.  Each inner list
     consists of three named elements: GOID, Ontology, and Evidence.

     The GOID element matches the GO identifier named in the outer list
     and is included for convenience when processing the data using
     'lapply'.

     The Ontology element indicates which of the three Gene Ontology
     categories this identifier belongs to.  The categories are
     biological process (BP), cellular component (CC), and molecular
     function (MF).

     The Evidence element contains a code indicating what kind of
     evidence supports the association of the GO identifier to the
     Entrez Gene 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 identifiers and GO information were
     obtained through their mappings to Entrez Gene identifiers. NAs
     are assigned to probe identifiers that can not be mapped to any
     Gene Ontology information. Mappings between Gene Ontology
     identifiers an Gene Ontology terms and other information are
     available in a separate data package named GO.

     Mappings were based on data provided by:

     Tair: <URL:
     ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_AG_array_elements-2006-07-14.txt>
     Tair: <URL:
     ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes>
     Tair: <URL:
     ftp://ftp.arabidopsis.org/home/tair/User_Requests/LocusPublished.02022007>
     Built: N/A

     Tair: <URL:
     ftp://ftp.arabidopsis.org/home/tair/Ontologies/Gene_Ontology/ATH_GO_GOSLIM.20070224.txt>
     Built: N/A

     Package built Fri Aug 24 17:42:16 2007

_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"]]

         }

