regressionplot          package:globaltest          R Documentation

_R_e_g_r_e_s_s_i_o_n _P_l_o_t _f_o_r _G_l_o_b_a_l _T_e_s_t

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

     Produces a plot which can be used to visualize the effect of
     specific samples on the test result produced by 'globaltest'.

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

     regressionplot(gt, geneset, sampleid, ...)

_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 to be plotted (only
          necessary if multiple genesets were tested).

sampleid: An optional vector of names or numbers of the samples of
          interest.

     ...: Any extra arguments will be forwarded to the plotting
          function.

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

     The regressionplot plots, for all pairs of samples, the covariance
     between the expression patterns against the covariance between
     their clinical outcomes. Each point in the plot therefore
     represents a pair of samples. A regression line is fitted through
     the samples, which visualizes the test result of the function
     'globaltest'. A steeply increasing slope indicates a high
     (possibly significant) value of the test statistic.

     An optional argument 'sampleid' can be supplied, giving sample
     numbers of possibly outlying arrays. In this case, all pairs of
     arrays involving one of the arrays in 'sampleid' is marked as a
     red cross, while the other pairs are marked as a blue dot. The
     blue line which is fitted through all points can now be compared
     to a red dotted line which is fitted though only the red crosses.

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

     'NULL' (no output).

_N_o_t_e:

     Regressionplot 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:

         # Breast cancer data (exprSet) from the Netherlands Cancer
         # Institute with annotation:
         data(vandeVijver)
         data(annotation.vandeVijver)

         gt <- globaltest(vandeVijver, "ESR1", annotation.vandeVijver)

         if (interactive()) {
           regressionplot(gt[1])
           regressionplot(gt[1], sampleid = "122")
         }

