KEGGNode-class           package:KEGGgraph           R Documentation

_C_l_a_s_s "_K_E_G_G_N_o_d_e"

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

     The class to present 'entry' element in KGML files and nodes in
     KEGG graphs

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the function 'parseEntry' and
     is not intended to be directly created by users.

_S_l_o_t_s:


     '_e_n_t_r_y_I_D': entryID, the 'id' attribute of 'entry' elements in KGML
          files. In each KGML file the entryID is specified by
          auto-increment integers, therefore entryIDs from two
          individual KGML files are not unique. However, if
          'expandGenes' option is specified in 'KEGGpathway2Graph'
          function, the unique KEGGID will replace the default integer
          as the new entryID, which is unique in biological context 

     '_n_a_m_e': Name of the node 

     '_t_y_p_e': Type of the node, use 'data(KEGGNodeType)' to see
          available values 

     '_l_i_n_k': URL link of the node

     '_r_e_a_c_t_i_o_n': Reaction of the node

     '_m_a_p': Map of the node

     '_d_i_s_p_l_a_y_N_a_m_e': Its display name, for example 'hsa:1432' is
          displayed as 'p38'

_M_e_t_h_o_d_s:


     _g_e_t_D_i_s_p_l_a_y_N_a_m_e 'signature(object = "KEGGNode")': get display name 

     _g_e_t_E_n_t_r_y_I_D 'signature(obj = "KEGGNode")': get entryID, in case of
          gene-expanded graphs this is the same as getKEGGID

     _g_e_t_K_E_G_G_I_D 'signature(object = "KEGGNode")': get KEGGID

     _g_e_t_T_y_p_e 'signature(object = "KEGGNode")': get the type of the node

     <-_n_a_m_e 'signature(object = "KEGGNode")': replace name 

     _g_e_t_C_o_m_p_o_n_e_n_t 'signature(obj = "KEGGNode")': returns entryID (the
          same as 'getEntryID'), for compatibility with
          'KEGGGroup-class'

     _s_h_o_w 'signature(object = "KEGGNode")': show method 

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

     Jitao David Zhang <URL: mailto:j.zhang@dkfz.de>

_R_e_f_e_r_e_n_c_e_s:

     KGML Document manual <URL: http://www.genome.jp/kegg/docs/xml/>

_S_e_e _A_l_s_o:

     'KEGGEdge-class', 'parseEntry'

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

     ## We show how to extract information from KEGGNode object
     sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
     pathway <- parseKGML(sfile)

     ns <- nodes(pathway)
     node <- ns[[1]]

     show(node)
     getName(node)
     getDisplayName(node)
     getEntryID(node)
     getKEGGID(node)

