summaryPlot             package:CGHbase             R Documentation

_V_i_s_u_a_l_i_z_a_t_i_o_n _o_f _a_C_G_H _p_r_o_f_i_l_e_s.

_D_e_s_c_r_i_p_t_i_o_n:

     This function creates a summary plot for aCGH profiles.

_U_s_a_g_e:

             summaryPlot(x, y, ...)

_A_r_g_u_m_e_n_t_s:

       x: An object of class 'cghCall'.

       y: This argument is not used and should be missing. 

     ...: Arguments 'plot'. 

_D_e_t_a_i_l_s:

     We find plotted on the x-axis the array probes sorted by
     chromosomal position. The vertical bars represent the average
     probability that the positions they cover are gained (green bars)
     or lost (red bars). The green bars represent gains, the red bars
     represent losses. When 4 levels have been used for calling,
     amplifications are indicated with a blue tickmark at the top of
     the plot.

_V_a_l_u_e:

     This function creates a plot.

_A_u_t_h_o_r(_s):

     Sjoerd Vosse & Mark van de Wiel

_R_e_f_e_r_e_n_c_e_s:

     Mark A. van de Wiel, Kyung In Kim, Sjoerd J. Vosse, Wessel N. van
     Wieringen, Saskia M. Wilting and Bauke Ylstra. CGHcall: calling
     aberrations for array CGH tumor profiles. _Bioinformatics, 23_,
     892-894.

_E_x_a_m_p_l_e_s:

              ## Not run: 
        data(Wilting)
        rawcgh <- make_cghSeg(Wilting)
        normalized <- normalize(rawcgh)
        segmented <- segmentData(normalized)
        called <- CGHcall(segmented)
        summaryPlot(called)
        
     ## End(Not run)

