cghRegions              package:CGHbase              R Documentation

_C_l_a_s_s _t_o _c_o_n_t_a_i_n _a_n_d _d_e_s_c_r_i_b_e _a_r_r_a_y _c_o_m_p_a_r_a_t_i_v_e _g_e_n_o_m_i_c _h_y_b_r_i_d_i_z_a_t_i_o_n _r_e_g_i_o_n_s _d_a_t_a.

_D_e_s_c_r_i_p_t_i_o_n:

     Container for aCGH regions data and experimental metadata.
     'cghRegions' class is derived from 'eSet', and requires a matrix
     named 'regions' as assayData member. Furthermore, columns named
     'Chromosome', 'Start', 'End', 'Nclone', and 'Avedist' are required
     as featureData members, containing region  and position
     information.

_E_x_t_e_n_d_s:

     Directly extends class 'eSet'.

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     'new('cghRegions', phenoData = [AnnotatedDataFrame],
     experimentData = [MIAME], annotation = [character], regions =
     [matrix], featureData = [AnnotatedDataFrame], ...) '

     An object of this class is generally obtained by running the
     function 'CGHregions'.

_S_l_o_t_s:

     Inherited from 'eSet':

     '_a_s_s_a_y_D_a_t_a': Contains matrices with equal dimensions, and with
          column number equal to 'nrow(phenoData)'. 'assayData' must
          contain a matrix 'regions' with rows represening regions and
          columns representing samples. Additional matrices of
          identical size (e.g., representing measurement errors) may
          also be included in 'assayData'. Class:'AssayData'

     '_p_h_e_n_o_D_a_t_a': See 'eSet'

     '_f_e_a_t_u_r_e_D_a_t_a': An 'AnnotatedDataFrame' with columns 'Chromosome',
          'Start', 'End', 'Nclone', and 'Avedist' containing region 
          and position information.

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': See 'eSet'

     '_a_n_n_o_t_a_t_i_o_n': See 'eSet'

_M_e_t_h_o_d_s:

     Class-specific methods.

     '_r_e_g_i_o_n_s(_c_g_h_R_e_g_i_o_n_s)', '_r_e_g_i_o_n_s(_c_g_h_R_e_g_i_o_n_s,_m_a_t_r_i_x)<-' Access and
          set elements named 'regions' in the 'AssayData-class' slot.

     '_c_h_r_o_m_o_s_o_m_e_s', '_b_p_s_t_a_r_t', '_b_p_e_n_d', '_n_c_l_o_n_e', '_a_v_e_d_i_s_t' Access the
          region and position information stored in 'featureData'

     _p_l_o_t._c_g_h_R_e_g_i_o_n_s Create a plot displaying chromosomes on the Y-axis
          and base pair position on the X-axis. A new region is
          displayed by a slight jump with respect to the previous
          region. Each region is displayed as a bi-colored segment, the
          lower and upper part of which correspond to the proportions
          pl and pg of samples with a loss (red) or gain (green),
          respectively. The color coding is displayed as well: 1: pl
          (pg) < 10%; 2: 10% = pl (pg) < 30%; 3:30% = pl (pg) < 50%; 4:
          pl (pg) = 50%.

     _f_r_e_q_u_e_n_c_y_P_l_o_t Create a frequency plot

     See 'eSet' for derived methods. Annotation functionality is not
     yet supported.

_A_u_t_h_o_r(_s):

     Sjoerd Vosse

_S_e_e _A_l_s_o:

     'eSet', 'cghRaw', 'cghSeg', 'cghCall'

_E_x_a_m_p_l_e_s:

             # create an instance of cghRegions
             new("cghRegions")
             
             # load an instance of cghRegions
             data(WiltingRegions)
                     
             # plot all region data
             plot.cghRegions(WiltingRegions)
             # make a frequency plot
             frequencyPlot(WiltingRegions)
             
             # extract the region values
             values <- regions(WiltingRegions)
             
             # get the names of the samples
             sampleNames(WiltingRegions)

