annaffyGO              package:annaffy              R Documentation

_S_u_b_s_e_t _o_f _a_n_n_o_t_a_t_i_o_n _d_a_t_a _f_i_l_e _f_o_r _G_O _i_n _t_h_e _h_g_u_9_5_a_v_2 _p_a_c_k_a_g_e

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

     This is an R environment (hash table lilke) object containing key
     and value pairs for the mappings between probe identifiers (key)
     and Gene Ontology information collected from Gene Ontology
     consortium. Keys can be accessed using ls(name of the environment)
     and values using get(key, name of the environment) or mget(keys,
     name of the environment). Each probe id is mapped to a list of one
     (mapped to none or one GO id) or more (mapped to more than one GO
     ids) elements. When a probe id is mapped to at lest one GO id,
     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" contains 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:  

_I_M_P inferred from mutant phenotype  

_I_G_I inferred from genetic interaction

_I_P_I inferred from physical interaction  

_I_S_S inferred from sequence similarity 

_I_D_A inferred from direct assay  

_I_E_P inferred from expression pattern  

_I_E_A inferred from electronic annotation  

_T_A_S traceable author statement  

_N_A_S non-traceable author statement  

_N_D no biological data available  

_I_C inferred by curator  

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

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

     Mappings were based on data provided by LocusLink

     Source data built: LocusLink built: January 13, 2004.<URL:
     ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz>. Package
     built: Wed Jan 14 22:11:05 2004 Contains 250 randomly selected
     probes

_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:

             require("annotate") || stop("annotate unavailable")
             xx <- ls(env = annaffyGO)
             if(length(xx) > 0){
                     # Using get for value of the first key
                     get(xx[1], annaffyGO )
                     #Using mget for a few keys
                     if(length(xx) >= 3){
                             mget(xx[1:3], annaffyGO, ifnotfound=NA )
                             #Using lookUp of annotate(> 1.3.4)
                             lookUp(xx[1:3],"annaffy","GO")
                     }
                     # Get GO ids. annotate >= 1.3.7
                     goids <- lookUp(ls(annaffyGO)[1], "annaffy", "GO")
                     if(!is.na(goids)){
                         # GO id of the first element
                         goids[[1]]$GOID
                         # Ontology category of the first element
                         goids[[1]]$Ontology
                         # Evidence code
                         goids[[1]]$Evidence
                     }
             }

