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 larger standardized test statistic (Q - EQ) / sd(Q) 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:

     Jelle J. Goeman, Jan Oosting, Anne-Marie Cleton-Jansen, Jakob, K.
     Anninga, Hans C. van Houwelingen (2005) Testing association of a
     pathway with survival. Bioinformatics 21, 1950-1957. See also the
     vignette Globaltest.pdf that comes with this package.

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

     'globaltest', 'permutations', '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)

         gt <- globaltest(vandeVijver, "StGallen", annotation.vandeVijver)

         sampling(gt, ndraws=100)

