getDisplayName-methods       package:KEGGgraph       R Documentation

_G_e_t _a _c_h_a_r_a_c_t_e_r _s_t_r_i_n_g _a_s _l_a_b_e_l _f_o_r _d_i_s_p_l_a_y

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

     In KGML files, 'graph' element has a 'name' attribute to store the
     displaying name of a node, which is straighforward for end users.
     For example, biologists have no idea about a node 'hsa:1432' but
     its display name 'MAPK14' helps them to link this node to their
     knowledge. This method extract DisplayName from graph objects for
     KEGGNode and graph, where the method for graph returns the display
     names of its nodes.

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


     _o_b_j_e_c_t = "_K_E_G_G_N_o_d_e" An object of 'KEGGNode-class' 

     _o_b_j_e_c_t = "_g_r_a_p_h" A KEGG graph object

_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/>

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

     sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
     pathway <- parseKGML(sfile)

     nodes <- nodes(pathway)
     subnodes <- nodes[10:15]

     sapply(subnodes, getDisplayName)
     ## compare them with getName, one 'displayName' may correspond to many paralogues
     sapply(subnodes, getName)

