checkerboard           package:globaltest           R Documentation

_C_h_e_c_k_e_r_b_o_a_r_d _p_l_o_t _f_o_r _G_l_o_b_a_l _T_e_s_t _r_e_s_u_l_t

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

     Produces a plot to visualize the test result produced by
     'globaltest', by showing the association between pairs of samples.

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

     checkerboard(testresult, sort = TRUE)

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

testresult: The output of a call to 'globaltest'.

    sort: A logical flag to indicate whether the samples should be
          sorted by the clinical outcome to give a clearer picture.

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

     The checkerboard shows the pairs of samples which have high
     covariance in white and the pairs with low covariance in black.
     This can be used to visualize the data and to search for outlying
     arrays.

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

     A matrix giving the old and the new sample numbers.

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

     Jelle Goeman: j.j.goeman@lumc.nl

_R_e_f_e_r_e_n_c_e_s:

     J. J. Goeman, S.A. van de Geer, F. de Kort and J. C. van
     Houwelingen, _A global test for association of a group of genes
     with a clinical outcome_, Technical Report MI 2003-03,
     Mathematical Institute, Leiden University. Available from  <URL:
     http://www.math.leidenuniv.nl/~jgoeman>.

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

     'globaltest', 'regressionplot', 'geneplot', 'permutations'.

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

     if(interactive()){
         data(exampleX)      # Expression data (40 samples; 1000 genes)
         data(exampleY)      # Clinical outcome for the 40 samples
         pathway <- 1:25     # A pathway contains genes 1 to 25
         gt <- globaltest(exampleX, exampleY, test.genes = pathway)
         gt
         checkerboard(gt)
     }

