permutations           package:globaltest           R Documentation

_H_i_s_t_o_g_r_a_m _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 histogram for visualization of the permutations used in
     'globaltest'.

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

     permutations(testresult)

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

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

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

     Produces a histogram of the value of the test statistic calculated
     for permutations of the clinical outcome, compared with the test
     statistic for the true clinical outcome.

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

     'NULL' (no output).

_N_o_t_e:

     Only works if the option 'permutation = TRUE' was chosen when
     calling 'globaltest'.

_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', 'checkerboard', 'geneplot', 'regressionplot'.

_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, 
                                                     permutation = TRUE)
         gt
         permutations(gt)
     }

