permutations           package:globaltest           R Documentation

_P_e_r_m_u_t_a_t_i_o_n_s _v_e_r_s_i_o_n _o_f _t_h_e _G_l_o_b_a_l _T_e_s_t

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

     Produces permutations of the 'globaltest' test statistic and uses
     these to recalculate the p-value.

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

     permutations(gt, geneset, 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(s) to be used (only
          necessary if multiple genesets were tested).

   nperm: The number of permutations to be used.

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

     A permutation p-value is calculated by comparing the value of the
     test statistic for random permutations of the clinical outcome to
     the value of the test statistic for the true clinical outcome. The
     permuted test statistics are stored for later visualisation using
     'hist'.

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

     An object of class 'gt.result'.

_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:

         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

         perm.gt <- permutations(gt)
         perm.gt

         if (interactive()) {
           hist(perm.gt)
         }

