translateKEGGgraph         package:KEGGgraph         R Documentation

_T_r_a_n_l_a_t_e _t_h_e _K_E_G_G _g_r_a_p_h _f_r_o_m _b_e_i_n_g _i_n_d_e_x_e_d _b_y _K_E_G_G_I_D _t_o _a_n_o_t_h_e_r
_i_d_e_n_t_i_f_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     The function translates the KEGG graph into a graph of equivalant
     topology while index with unique identifiers given by user. The
     new identifiers could be, for example, GeneSymbol or other
     identifiers mapped to KEGGID.

_U_s_a_g_e:

     translateKEGGgraph(graph, newNodes)

_A_r_g_u_m_e_n_t_s:

   graph: A KEGG graph 

newNodes: A character vector giving the new nodes, must be of the same
          length and same order of the nodes of the given graph 

_D_e_t_a_i_l_s:

     The function is still experimental and users are welcomed to
     report any difficulties

_V_a_l_u_e:

     Another graph indexed by the given identifier

_A_u_t_h_o_r(_s):

     Jitao David Zhang <j.zhang@dkfz.de>

_E_x_a_m_p_l_e_s:

     sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
     gR <- parseKGML2Graph(sfile,expandGenes=TRUE)

     subG <- subKEGGgraph(c("hsa:1848","hsa:1432","hsa:2002","hsa:8986"),gR)
     symbols <- c("DUSP6","MAPK14","ELK1","RPS6KA4")
     sub2G <- translateKEGGgraph(subG, symbols)
     sub2G
     nodes(sub2G)

     if(require(Rgraphviz) & interactive()) {
     plot(sub2G, "neato")
     }

