hgu133aPATH             package:hgu133a             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. hgu133aPATH 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 id. Pathway name for a given
     pathway id 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
     ids as keys.   

     Mappings were based on data provided by:

     KEGG:<URL:
     http://gopher5/compbio/annotationSourceData/kegg/pathways>. Built:
     Release 34.0 (April 2005)

     Entrez Gene:<URL:
     http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/g
     ene/DATA/>. Built: Source data downloaded from Entrez Gene on Tue
     May 17 12:53:16 2005

     Package built Tue May 17 13:02:12 2005

_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(hgu133aPATH)
         # Remove probe ids that do not map to any pathway id
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
             # The pathway ids for the first two elements of XX
             xx[1:2]
             # Get the first one
             xx[[1]]
         } 

