hgu133aGO2ALLPROBES         package:hgu133a         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 _b_y _a_l_l _p_r_o_b_e _i_d_s _c_o_r_r_e_s_p_o_n_d_i_n_g _t_o _t_h_e _G_O
_i_d_s

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

     A GO id can be associated with a group of genes directly or
     indirectly through the children GO ids. hgu133aGO2ALLPROBES maps
     GO ids to genes (represented by probe ids) that are directly or
     indirectly mapped to the GOs through various approaches

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

     hgu133aGO2ALLPROBES is an environment object with key and value
     pairs. Keys are GO ids and values are all the probe ids that are
     mapped to the GO ids directly or indirectly. Values are vectors of
     length 1 or greater depending on whether a given GO id can be
     mapped to only one or more probe ids. Names for values are the
     evidence codes for the GO ids indicating what kind of evidence is
     found to support the association). 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

     GO ids can not be mapped to any probe identifier are assigned a
     value of NA. A GO id may be mapped to the same probe id more than
     once but the evidence code can be different. 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:

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

     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(hgu133aGO2ALLPROBES)
         if(length(xx) > 0){
             # Gets the probe ids for the top 2nd and 3nd GO ids
             goids <- xx[2:3]
             # Gets all the probe ids for the first element of goids
             goids[[1]]
             # Evidence code for the mappings
             names(goids[[1]])
         }

