plotProfile             package:CGHcall             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 plot for aCGH profiles, including raw
     log2ratios, segments and calls.

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

     plotProfile(CGHcall.result, samples="all", export="no")
     plotSummary(CGHcall.result, samples="all", export="no")

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

CGHcall.result: The list of results that is returned by 'CGHcall'.

 samples: Which samples to plot. Either 'all' or a numerical vector. 

  export: Whether a postscript file should be exported. Either 'no' or
          a filename.

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

     For 'plotProfile' we find plotted on the x-axis the array probes
     sorted by chromosomal position. The black dots represent the
     normalized log2ratios (values are on the y-axis on the right
     side). The horizontal blue lines are the segments. The vertical
     bars represent the probability that the probes they cover are
     aberrations. The green bars represent gains, the red bars
     represent losses. If a bar crosses the middle horizontal line
     (probability of 0.5), the probes in this region are said to be
     aberrated. When 4 levels have been used for calling,
     amplifications are indicated with a blue tickmark at the top of
     the plot.

     For 'plotSummary' 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:

       data(Wilting)
       ## First preprocess the data
       raw.data <- preprocess(Wilting, type="dataframe")
       ## Simple global median normalization for samples with 75% tumor cells
       perc.tumor <- rep(0.75, 3)
       normalized.data <- normalize(raw.data, cellularity=perc.tumor)
       ## Segmentation with slightly relaxed significance level to accept change-points.
       ## Note that segmentation can take a long time.
       ## Not run: segmented.data <- segmentData(normalized.data, alpha=0.02)
       ## Call aberrations
       ## Not run: result <- CGHcall(normalized.data, segmented.data)
       ## Create a plot for the first sample and export it to a file
       ## Not run: plotProfile(result, samples=1, export='plot_1.ps')
       ## Create a summary plot including the first and third sample
       ## Not run: plotSummary(result, samples=c(1,3), export='summary_1_3.ps')  

