permutations           package:globaltest           R Documentation

_P_e_r_m_u_t_a_t_i_o_n_s _P_l_o_t _f_o_r _G_l_o_b_a_l _T_e_s_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(gt, geneset = NULL, nperm = 10^4)

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

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

 geneset: The name or number of the geneset to be plotted  (only
          necessary if multiple genesets were tested).

   nperm: The number of permutations to be used.

_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 except the plot).

_N_o_t_e:

     Permutations does not work if the adjusted version of  globaltest
     was used.

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

     Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting

_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, 2004, _A global test for groups of genes:  testing
     association with a clinical outcome_,  _Bioinformatics_ 20 (1)
     93-99. See also the How To  Globaltest.pdf included with this
     package.

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

     'globaltest', 'sampleplot', 'geneplot'.

_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)
     }

