org.EcK12.egPATH       package:org.EcK12.eg.db       R Documentation

_M_a_p_p_i_n_g_s _b_e_t_w_e_e_n _E_n_t_r_e_z _G_e_n_e _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.EcK12.egPATH maps entrez gene
     identifiers to the identifiers used by KEGG for pathways

_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.EcK12.egPATH
         # Get the entrez gene 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]]
         }

         # For the reverse map:
         # Convert the object to a list
         xx <- as.list(org.EcK12.egPATH2EG)
         # Remove pathway identifiers that do not map to any entrez gene id
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
             # The entrez gene identifiers for the first two elements of XX
             xx[1:2]
             # Get the first one
             xx[[1]]
         }

