aafPathwayItem-class         package:annaffy         R Documentation

_C_l_a_s_s _a_a_f_P_a_t_h_w_a_y_I_t_e_m, _a _c_l_a_s_s _f_o_r _K_E_G_G _p_a_t_h_w_a_y _i_d _e_l_e_m_e_n_t_s

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

     An abstraction for KEGG pathway id elements from Bioconductor data
     packages. Multiple instances of this class are held by the wrapper
     class 'aafPathway'.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects are generally created by the 'aafPathway' constructor.
     Objects can also be created manually by calls of the form
     'new("aafPathwayItem", id, name, enzyme)'.

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


     '_i_d': Object of class 'character' containing KEGG pathway id

     '_n_a_m_e': Object of class 'character' containing textual name

     '_e_n_z_y_m_e': Object of class 'character' containing the Enzyme
          Commision number if applicable


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


     _g_e_t_T_e_x_t (aafPathwayItem): Returns textual representation formatted
          "'id': 'name'".

     _g_e_t_U_R_L (aafPathwayItem): Returns a URL to the corresponding entry
          in the Kyoto Encyclopedia of Genes and Genomes database. If
          there is a corresponding EC number, it will be highlighted in
          red.

     _g_e_t_H_T_M_L (aafPathwayItem): Returns an HTML representation including
          the URL link and pathway name.


_A_u_t_h_o_r(_s):

     Colin A. Smith, annaffy@colinsmith.org

_S_e_e _A_l_s_o:

     aafPathway-class, aafPathway

