cghSeg                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 _s_e_g_m_e_n_t_e_d _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 _d_a_t_a.

_D_e_s_c_r_i_p_t_i_o_n:

     Container for aCGH data and experimental metadata. 'cghSeg' class
     is derived from 'eSet', and requires a matrix named 'copynumber'
     as well as a  matrix named 'segmented' as assayData members of
     equal dimensions.  Furthermore, columns named 'Chromosome',
     'Start', and 'End' are  required as featureData members,
     containing feature 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('cghSeg', phenoData = [AnnotatedDataFrame], experimentData =
     [MIAME], annotation = [character], copynumber = [matrix],
     segmented = [matrix], featureData = [AnnotatedDataFrame], ...) '

     An object of class 'cghSeg' is generally obtained as output from
     'segmentData'.

_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 matrices 'copynumber' and 'segmented' with rows
          represening array probes and columns representing samples.
          Additional matrices of identical size (e.g., representing
          measurement errors) may also be included in 'assayData'.
          Class:'AssayData-class'

     '_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', and 'End' containing array element position  data.

     '_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.

     '_c_o_p_y_n_u_m_b_e_r(_c_g_h_S_e_g)', '_c_o_p_y_n_u_m_b_e_r(_c_g_h_S_e_g,_m_a_t_r_i_x)<-' Access and set
          elements named 'copynumber' in the 'AssayData-class' slot.

     '_s_e_g_m_e_n_t_e_d(_c_g_h_S_e_g)', '_s_e_g_m_e_n_t_e_d(_c_g_h_S_e_g,_m_a_t_r_i_x)<-' Access and set
          elements named 'segmented' 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' Access the chromosomal positions
          stored in 'featureData'

     _p_l_o_t._c_g_h_S_e_g Create a plot containing log2ratios and segments
          ordered by chromosomal position

     See 'eSet' for derived methods.

_A_u_t_h_o_r(_s):

     Sjoerd Vosse

_S_e_e _A_l_s_o:

     'eSet-class', 'cghRaw-class', 'cghCall-class'

_E_x_a_m_p_l_e_s:

             # create an instance of cghSeg
             new("cghSeg")
             
             # load an instance of cghSeg
             data(WiltingSeg)

             # plot the first sample
             # plot.cghSeg(WiltingSeg[,1])
             # first three chromosomes
             # plot.cghSeg(WiltingSeg[chromosomes(WiltingSeg)==1,1])
             
             # get the copynumber values of the third and fourth sample
             log2ratios <- copynumber(WiltingSeg[,3:4])
             
             # get the names of the samples
             sampleNames(WiltingSeg)
             
             # get the names of the array elements
             featureNames(WiltingSeg)

