PWAmat               package:annotate               R Documentation

_A _f_u_n_c_t_i_o_n _t_o _c_o_m_p_u_t_e _t_h_e _p_r_o_b_e _t_o _K_E_G_G _p_a_t_h_w_a_y _i_n_c_i_d_e_n_c_e _m_a_t_r_i_x.

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

     For a given chip we compute the mapping from probes to KEGG
     pathways.

_U_s_a_g_e:

     PWAmat(data)

_A_r_g_u_m_e_n_t_s:

    data: The name of the chip for which the incidence matrix should be
          computed.

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

     Not much to say, just find which probes are in which pathways and
     return the incidence matrix, with pathways as rows and probes as
     columns. 

     It would be nice to be able to specify a set of probes to use, so
     that  one does not do perform the calculations using all probes if
     they are not of interest.

_V_a_l_u_e:

     A matrix containing zero or one, depending on whether the probe
     (row) is in a pathway (column).

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

     R. Gentleman

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

     'KEGG2heatmap', 'GOmnplot'

_E_x_a_m_p_l_e_s:

       if(require("hgu95av2") ) {
         Am1 = PWAmat("hgu95av2")
      }

