aafPathway-class           package:annaffy           R Documentation

_C_l_a_s_s _a_a_f_P_a_t_h_w_a_y, _a _c_l_a_s_s _f_o_r _K_E_G_G _p_a_t_h_w_a_y _i_d_s

_D_e_s_c_r_i_p_t_i_o_n:

     An abstraction for KEGG pathway ids from Bioconductor data
     packages. This class is actually extends 'aafList' and holds
     'aafPathwayItem' objects which have the actual annotation data.

_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("aafPathway", list(pathwayitems))'.

_S_l_o_t_s:

     '._D_a_t_a': Object of class 'list'

_E_x_t_e_n_d_s:

     Class 'aafList', from data part.

_M_e_t_h_o_d_s:

     _g_e_t_T_e_x_t (aafGO): Returns a comma delimeted list of the individual
          'aafPathwayItem' objects.

     _g_e_t_U_R_L (aafGO): Returns zero length character vector because this
          method is not valid for this class.

     _g_e_t_H_T_M_L (aafGO): Returns an HTML representation of each of the
          individual 'aafPathwayItem' objects, concatenated together.

     _g_e_t_T_D (aafGO): Returns an HTML table cell representation with the
          class set to "aafPathway".

     _g_e_t_C_S_S (aafGO): Returns a line of CSS which intends PathwayItem
          paragraphs.

_A_u_t_h_o_r(_s):

     Colin A. Smith, annaffy@colinsmith.org

_S_e_e _A_l_s_o:

     aafPathway, aafPathwayItem, aafList