geneplot             package:globaltest             R Documentation

_G_e_n_e_p_l_o_t _f_o_r _G_l_o_b_a_l _T_e_s_t _r_e_s_u_l_t

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

     Produces a plot to show the influence of individual genes on the
     test result produced by 'globaltest'.

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

     geneplot(testresult)

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

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

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

     The geneplot shows a bar an a reference line for each gene. The
     bar shows the influence of each gene on the test result; the
     reference line shows the expected influence if the gene was not
     associated with the outcome. The color of the bar indicates
     positive or negative correlation of the gene with the clinical
     outcome, to distinguish between up and downregulation.

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

     If gene names were supplied in the call to  'globaltest', geneplot
     returns a data.frame referring  the gene names to the gene numbers
     appearing in the plot.  Otherwise 'NULL'.

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

     Jelle Goeman: j.j.goeman@lumc.nl

_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, _A global test for association of a group  of genes
     with a clinical outcome_, Technical Report MI 2003-03, 
     Mathematical Institute, Leiden University. Available from  <URL:
     http://www.math.leidenuniv.nl/~jgoeman>.

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

     'globaltest', 'regressionplot', 'checkerboard', 'permutations'.

_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)
         gt
             geneplot(gt)
     }

