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 using permutations of the clinical outcome to the
     value of the test statistic for the true clinical outcome. If the
     number of possible permutations is smaller than the value of
     'nperm', all possible permutations are used, otherwise 'nperm'
     random permutations. 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:

     For references, type: citation("globaltest"). See also the
     vignette GlobalTest.pdf included with this package.

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

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

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

         # Breast cancer data (ExpressionSet) from the Netherlands Cancer
         # Institute with annotation:
         data(vandeVijver)
         data(annotation.vandeVijver)
         aPathway <- annotation.vandeVijver[1]

         gt <- globaltest(vandeVijver, "StGallen", aPathway)
         perm.gt <- permutations(gt)

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

