sampling             package:globaltest             R Documentation

_S_a_m_p_l_i_n_g _r_a_n_d_o_m '_p_a_t_h_w_a_y_s' _f_o_r _t_h_e _G_l_o_b_a_l _T_e_s_t

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

     For every pathway in a result of 'globaltest',  calculates how
     many randomly drawn groups of genes of the same size have a 
     smaller or equal p-value.

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

     sampling(gt, geneset, ndraws = 10^3)

_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).

  ndraws: The number of random pathways to be used.

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

     For every pathway in 'gt[geneset]', a number 'ndraws' random
     'pathways' is selected by randomly sampling sets of genes of the
     same  size as the tested pathway. A 'comparative p-value' is
     calculated by counting  what proportion of the random pathways has
     a smaller or equal p-value than  the tested pathway.

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

     An object of class  'gt.result'.

_N_o_t_e:

     The function 'sampling' cannot be applied to a  'gt.result' object
     resulting from a call to  'permutations'.

_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', 'permutations', '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 <- sampling(globaltest(exampleX, exampleY, test.genes = pathway))
         gt

