KEGGpathway2reactionGraph     package:KEGGgraph     R Documentation

_C_o_n_v_e_r_t _c_h_e_m_i_c_a_l _r_e_a_c_t_i_o_n _n_e_t_w_o_r_k _o_f _K_E_G_G _p_a_t_h_w_a_y _i_n_t_o _g_r_a_p_h

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

     Regulatory pathways are always viewed as protein networks, so
     there is no 'reaction' information saved in their KGML files.
     Metabolic pathways are viewed both as both protein networks and
     chemical networks, hence the 'KEGGPathway-class' object may have
     reactions information among chemical compounds.

     This functions extracts reaction information from KEGG pathway,
     and convert the chemical compound reaction network into directed
     graph.

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

     KEGGpathway2reactionGraph(pathway, uniqueReaction = TRUE)

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

 pathway: A 'KEGGPathway-class' object, usually as the result of the
          function 'parseKGML'

uniqueReaction: logical, to indicate whether several chemical reactions
          (identified by different KEGG reaction ID) should be treated
          as one (TRUE) or many (FALSE)

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

     The direction of the graph is specified by the role of the
     compound in the reaction, the edges goes always out of 'substrate'
     and points to 'product'. 

     For now there is no wrapper to parse the KGML file directly into a
     reaction graph. In future there maybe one, but we don't want to
     confuse users with two similar functions to parse the file into a
     graph (since we assume that most users will need the protein
     graph, which can be conveniently parsed by 'parseKGML2Graph').

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

     A directed graph with compounds as nodes and reactions as edges.

_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:

     'KEGGPathway-class'

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

     mapfile <-  system.file("extdata/map00260.xml",package="KEGGgraph")
     map <- parseKGML(mapfile)
     cg <- KEGGpathway2reactionGraph(map, uniqueReaction=FALSE)
     cg
     nodes(cg)[1:3]
     edges(cg)[1:3]

