KEGGReaction-class         package:KEGGgraph         R Documentation

_C_l_a_s_s "_K_E_G_G_R_e_a_c_t_i_o_n"

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

     A class to present 'reaction' elements in KGML files

_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 'parseReaction'.

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


     '_n_a_m_e': Object of class '"character"' the KEGGID of this reaction,
          e.g. "rn:R02749"

     '_t_y_p_e': Object of class '"character"' the type of this reaction,
          either 'reversible' or 'irreversible'

     '_s_u_b_s_t_r_a_t_e_N_a_m_e': Object of class '"character"', KEGG identifier of
          the COMPOUND database or the GLYCAN database e.g.
          "cpd:C05378"

     '_s_u_b_s_t_r_a_t_e_A_l_t_N_a_m_e': Object of class '"character"' alternative name
          of its parent substrate element 

     '_p_r_o_d_u_c_t_N_a_m_e': Object of class '"character"' specifies the KEGGID
          of the product

     '_p_r_o_d_u_c_t_A_l_t_N_a_m_e': Object of class '"character"' alternative name
          of its parent product element 

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


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

     _g_e_t_N_a_m_e 'signature(object = "KEGGReaction")': get the KEGGID of
          the reaction

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

     _g_e_t_S_u_b_s_t_r_a_t_e 'signature(object = "KEGGReaction")': get the name of
          substrate

     _g_e_t_P_r_o_d_u_c_t 'signature(object = "KEGGReaction")': get the name of
          product

_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:

     ## We show how to extract reactions from a 'KEGGPathway' object
     mapfile <- system.file("extdata/map00260.xml", package="KEGGgraph")

     maptest <- parseKGML(mapfile)
     mapReactions <- getReactions(maptest)

     ## More details about reaction
     reaction <- mapReactions[[1]]
     getName(reaction)
     getType(reaction)
     getSubstrate(reaction)
     getProduct(reaction)

