lemmaPlots               package:lemma               R Documentation

_L_E_M_M_A - _d_i_a_g_n_o_s_t_i_c_s _p_l_o_t_s

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

     This program produces two diagnostics plots for the two fitting
     procedures in the  LEMMA model.

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

      lemmaPlots(outdir, mgq=0.99, titletext, modes) 

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

  outdir: The directory containing the RData file with the saved
          estimates and data from a previous invocation of lemma().
          Default=`OUT' 

     mgq: The quantile used for plotting the m_g histogram.  Genes with
           m_g values outside the mgq quantile are excluded from the
          plot.  Default=0.99

titletext: The title of the plot

   modes: The number of assumed (null + nonnull) groups. Can be either
          2 or 3 (default=3). 

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

     The function lemmaPlots generates two plots on one page, and saves
     them in postscript and pdf formats under the 'outdir' directory.

     (a) a histogram of the d_g statistics and the fitted curves for
     the null and nonnull groups, as well as the mixture (using the
     average error variance).

     (b) a histogram of m_g, and the fitted distribution, based on the
     estimates for alpha and beta.

     Note - we are using ps2pdf to convert the postscript format to
     pdf. It is assumed to be installed on the computer.

