KEGGPathway-class         package:KEGGgraph         R Documentation

_C_l_a_s_s "_K_E_G_G_P_a_t_h_w_a_y"

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

     A class to represent KEGG pathway

_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 form 'new("KEGGPathway",
     ...)' . Normally they are created by 'parseKGML'.

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


     '_p_a_t_h_w_a_y_I_n_f_o': An object of 'KEGGPathwayInfo-class'

     '_n_o_d_e_s': List of objects of 'KEGGNode-class'

     '_e_d_g_e_s': List of objects of 'KEGGEdge-class' 

     '_r_e_a_c_t_i_o_n_s': List of objects of 'KEGGReaction-class' 

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


     _e_d_g_e_s 'signature(object = "KEGGPathway", which = "ANY")':
          KEGGEdges of the pathway

     _e_d_g_e_s<- 'signature(object = "KEGGPathway")': setting edges

     _g_e_t_N_a_m_e 'signature(object = "KEGGPathway")': getting pathway name 

     _g_e_t_T_i_t_l_e 'signature(object = "KEGGPathway")': getting pathway
          title 

     _n_o_d_e_s<- 'signature(object = "KEGGPathway", value = "ANY")':
          setting nodes

     _n_o_d_e_s 'signature(object = "KEGGPathway")': KEGGNodes of the
          pathway 

     _g_e_t_P_a_t_h_w_a_y_I_n_f_o 'signature(object = "KEGGPathway")': getting
          KEGGPathwayInfo

     _g_e_t_T_i_t_l_e 'signature(object = "KEGGPathway")': getting title of the
          pathway 

     _s_h_o_w 'signature(object = "KEGGPathway")': display 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:

     'parseKGML', 'KEGGEdge-class', 'KEGGNode-class',
     'KEGGReaction-class'

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

     ## We show how to extract information from KEGGPathway objects
     ## Parse KGML file into a 'KEGGPathway' object
     mapfile <- system.file("extdata/map00260.xml", package="KEGGgraph")
     maptest <- parseKGML(mapfile)

     ## short summary of the pathway
     maptest

     ## get information of the pathway
     getPathwayInfo(maptest)

     ## nodes of the pathway
     nodes <- nodes(maptest)
     node <- nodes[[3]]
     getName(node)
     getType(node)
     getDisplayName(node)

     ## edges of the pathway
     edges <- edges(maptest)
     edge <- edges[[3]]
     getEntryID(edge)
     getSubtype(edge)

