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
     (column) is in a pathway (row).

_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")
      }