plot.MACATevalScoring         package:macat         R Documentation

_P_l_o_t _f_u_n_c_t_i_o_n _f_o_r _M_A_C_A_T_e_v_a_l_S_c_o_r_i_n_g _o_b_j_e_c_t_s.

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

     Function plots scores, 0.025 and 0.975 quantiles of the permuted
     scores (grey lines), and sliding average score (red line) along
     the chromosome. Yellow dots highlight regions, in which the
     smoothed absolute scores exceed the permutation-derived quantile
     boundaries.

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

     ## S3 method for class 'MACATevalScoring':
     plot(x, output = "x11", 
                   HTMLfilename = NULL, mytitle = NULL, new.device = TRUE, ...)

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

       x: MACATevalScoring object.

  output: plot "x11" or create a "html" -file with further information.
          HTML-page will open automatically.

HTMLfilename: HTML-filename, default:'Results<CHOMOSOME>_<CLASS>.html'

 mytitle: Title of HTML-page, default: Results of class <CLASS> on
          chromosome <CHROMOSOME>

new.device: if FALSE: Possibility to plot several plots in one device

     ...: further arguments passed on to generic function 'plot'

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

     One can create a HTML-page on-the-fly if argument output='html'. 
     The HTML-page provides informations about highlighted regions in
     the plot.  Furthermore there are click-able Entrezgene-IDs for
     further analysis.

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

     MACAT development team

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

     'evalScoring', 'getResults'

_E_x_a_m_p_l_e_s:

      # see function 'evalScoring' for an example

