GenericArray-class       package:GenomeGraphs       R Documentation

_C_l_a_s_s "_G_e_n_e_r_i_c_A_r_r_a_y", _r_e_p_r_e_s_e_n_t_i_n_g _a_r_r_a_y _d_a_t_a

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

     The Generic Array class is a class that can be used to create
     plots from array data such as microarrays and arrayCGH platforms.
     It can represent,  the data as line plots or dot plots and
     segments can be included as well

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("GenericArray",
     ...)'.

_S_l_o_t_s:


     '_i_n_t_e_n_s_i_t_y': Object of class '"matrix"', matrix containing the
          intensities of expression or cgh data.  Rows should be
          probes, columns samples

     '_p_r_o_b_e_S_t_a_r_t': Object of class '"numeric"', start position of the
          probes

     '_p_r_o_b_e_E_n_d': Object of class '"numeric"', end position of the
          probes if available

     '_t_y_p_e': Object of class '"character"', has two values: line and
          point.  If line is selected then a line will be plotted for
          each sample.  If point is selected. points will be plotted.

     '_s_e_g_m_e_n_t_s': Object of class '"list"', if segments are available
          they have to be represented as a list, each position in the
          list should correspond to each sample as defined by the
          columns of the intensity matrix 

     '_s_e_g_m_e_n_t_S_t_a_r_t': Object of class '"list"', containing the start
          positions of the segments

     '_s_e_g_m_e_n_t_E_n_d': Object of class '"list"', containing the end
          positions of the segments 

     '_c_o_l_o_r': Object of class '"character"', represents the color to be
          used to plot the intensity matrix, can be a vector of colors
          for multiple samples 

     '_l_t_y': Object of class '"character"',if line is selected as type,
          lty specifies which line type should be used.  Can be a
          vector of line types for multiple samples

     '_p_c_h': Object of class '"numeric"', if point is selected as type
          then pch represents which symbol should be used to plot the
          points

     '_p_o_i_n_t_S_i_z_e': Object of class '"numeric"', specifies the point size
          if point is selected as type

     '_l_w_d': Object of class '"numeric"', specifies the line width if
          line is selected as type.  Can be a vector of line widths if
          multple samples are present

     '_s_i_z_e': Object of class '"numeric"' representing the size of the
          Array plot in the final plot

     '_s_e_g_m_e_n_t_C_o_l_o_r': Object of class '"character"'. If segments are to
          be plotted, this will define the color of the segment lines 

_M_e_t_h_o_d_s:


     _s_h_o_w 'signature(object = "GenericArray")': ... 

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

     Steffen Durinck

_R_e_f_e_r_e_n_c_e_s:

     http://www.stat.berkeley.edu/~steffen/

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

     objects to See Also as 'gdPlot'

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

     if(interactive()){
     data("dummyData", package="GenomeGraphs")

     minbase <- 180292097 
     maxbase <- 180492096
     ideog <- new("Ideogram", chromosome = "3")
     expres <- new("GenericArray", intensity = intensity, probeStart = exonProbePos, 
                   dp = DisplayPars(color="darkred", type="point"))
     gdPlot(list(ideog, expres), minBase = minbase, maxBase =maxbase)
     }

