org.Sc.sgdPATH         package:org.Sc.sgd.db         R Documentation

_M_a_p_p_i_n_g_s _b_e_t_w_e_e_n _O_R_F _i_d_e_n_t_i_f_i_e_r_s _a_n_d _K_E_G_G _p_a_t_h_w_a_y _i_d_e_n_t_i_f_i_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway
     data for various organisms. org.Sc.sgdPATH maps ORF identifiers to
     the identifiers used by KEGG for pathways.  The reverse map
     org.Sc.sgdPATH2ORF maps back from KEGG pathway IDs to the ORF
     identifiers.

_D_e_t_a_i_l_s:

     Each KEGG pathway has a name and identifier. Pathway name for a
     given pathway identifier can be obtained using the KEGG data
     package that can either be built using AnnBuilder or downloaded
     from Bioconductor <URL: http://www.bioconductor.org>.

     Graphic presentations of pathways are searchable at
     url{http://www.genome.ad.jp/kegg/pathway.html} by using pathway
     identifiers as keys.   

     Mappings were based on data provided by: KEGG GENOME (
     ftp://ftp.genome.jp/pub/kegg/genomes ) on 2008-Sep2

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.genome.ad.jp/kegg/>

_E_x_a_m_p_l_e_s:

         x <- org.Sc.sgdPATH
         # Get the ORF identifiers that are mapped to a KEGG pathway ID
         mapped_genes <- mappedkeys(x)
         # Convert to a list
         xx <- as.list(x[mapped_genes])
         if(length(xx) > 0) {
           # Get the PATH for the first five genes
           xx[1:5]
           # Get the first one
           xx[[1]]
         }
         # Convert the object to a list
         xx <- as.list(org.Sc.sgdPATH2ORF)
         # Remove pathway identifiers that do not map to any ORF id
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
             # The ORF identifiers for the first two elements of XX
             xx[1:2]
             # Get the first one
             xx[[1]]
         }

