getReactions-methods        package:KEGGgraph        R Documentation

_G_e_t _K_E_G_G _r_e_a_c_t_i_o_n_s

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

     In KGML, the pathway element specifies one graph object with the
     _entry_ elements as its nodes and the _relation_ and _reaction_
     elements as its edges. The _relation_ elements are saved as
     _edges_ in objects of 'KEGGPathway-class', and the _reactions_
     elements are saved as a slot of the object, which can be retrieved
     with the function 'getReactions'.

     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.

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


     _o_b_j_e_c_t = "_K_E_G_G_P_a_t_h_w_a_y" An object of 'KEGGPathway-class'

_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")
     maptest <- parseKGML(mapfile)
     maptest

     mapReactions <- getReactions(maptest)
     mapReactions[1:3]

