illuminaRatv1PATH       package:illuminaRatv1       R Documentation

_M_a_p_p_i_n_g_s _b_e_t_w_e_e_n _p_r_o_b_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. illuminaRatv1PATH maps probe
     identifiers to the identifiers used by KEGG for pathways in which
     the genes represented by the probe identifiers are involved

_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:\<URL:
     ftp://ftp.genome.ad.jp/pub/kegg/tarfiles/pathway.tar.gz>. Built:
     Release 41.1, February 1, 2007

     Entrez Gene:\<URL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/>. Built:
     Source data downloaded from Entrez Gene on Wed Apr  4 12:02:34
     2007

     Package built Wed Apr  4 12:25:16 2007

_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:

         # Convert the environment to a list
         xx <- as.list(illuminaRatv1PATH)
         # Remove probe identifiers that do not map to any pathway id
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
             # The pathway identifiers for the first two elements of XX
             xx[1:2]
             # Get the first one
             xx[[1]]
         } 

