ipDataSource-class     package:domainsignatures     R Documentation

_A _c_l_a_s_s _t_o _s_t_o_r_e _m_a_p_p_i_n_g _i_n_f_o_r_m_a_t_i_o_n _b_e_t_w_e_e_n _g_e_n_e_s, _p_a_t_h_w_a_y_s _a_n_d
_i_n_t_e_r_P_r_o _d_o_m_a_i_n_s

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

     This class represents the data necessary to run 'gseDomain'

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

     You should always create these objects using either one of the
     functions 'dataSource' or 'getKEGGdata'.

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     Objects can be created using
      '  new('ipDataSource','
      '    genes        = ...., # Object of class character'
      '    pathways     = ....  # Object of class character'
      '    domains      = ....  # Object of class character'
      '    gene2Domains = ....  # Object of class environment'
      '    path2Domains = ....  # Object of class environment'
      '    type         = ...., # Object of class character'
      '  )'
      or the functions 'dataSource' or 'getKEGGdata'.

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


     '_g_e_n_e_s': Vector of unique entrezgene identifiers

     '_p_a_t_h_w_a_y_s': Vector of unique pathway identifiers

     '_d_o_m_a_i_n_s': Vector of unique InterPro identifiers

     '_g_e_n_e_2_D_o_m_a_i_n_s': Hash table mapping entrezgene IDs to Interpro IDs

     '_p_a_t_h_2_D_o_m_a_i_n_s': Hash table mapping pathway IDs to InterPro IDs

     '_t_y_p_e': Type of pathway. A character skalar

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


     _s_h_o_w display summary.

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

     Florian Hahne

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

     'dataSource' or 'getKEGGdata'

