agPATH                  package:ag                  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. agPATH 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 18:26:20 2005

     Package built Tue May 17 18:29:49 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(agPATH)
         # 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]]
         } 

