makeExonArray          package:GenomeGraphs          R Documentation

_C_r_e_a_t_e_s _a_n_d _o_b_j_e_c_t _o_f _c_l_a_s_s _E_x_o_n_A_r_r_a_y

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

     Creates an object of class ExonArray, representing exon array
     microarray data

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

     makeExonArray(intensity, probeStart, probeEnd, probeId, nProbes, displayProbesets = FALSE, dp = NULL)

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

intensity: Matrix of intentsities, probes in the rows, samples in the
          columns 

probeStart: Vector of probe start positions

probeEnd: Vector of probe end positions (optional)

 probeId: Character vector containing the probe identifiers

 nProbes: Vector indicating how many probes are in each probeset

displayProbesets: Logical indicating if the probeset idenifier should
          be displayed or not

      dp: Object of class DisplayPars to set the display parameters

_V_a_l_u_e:

     Object of ExonArray class

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

     Steffen Durinck and Jim Bullard

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

     ~put references to the literature/web site here ~

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

     'gdPlot'

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

     ##---- Should be DIRECTLY executable !! ----
     ##-- ==>  Define data, use random,
     ##--    or do  help(data=index)  for the standard data sets.

     ## The function is currently defined as
     function (intensity, probeStart, probeEnd, probeId, nProbes, 
         displayProbesets = FALSE, dp = NULL) 
     {
         pt <- getClass("ExonArray")@prototype
         if (is.null(dp)) 
             dp <- pt@dp
         if (missing(probeEnd)) 
             probeEnd <- pt@probeEnd
         if (missing(probeId)) 
             probeId <- pt@probeId
         if (missing(nProbes)) 
             nProbes <- pt@nProbes
         if (is.null(dp)) 
             dp <- getClass("ExonArray")@prototype@dp
         new("ExonArray", intensity = intensity, probeStart = probeStart, 
             probeEnd = probeEnd, probeId = probeId, nProbes = nProbes, 
             displayProbesets = displayProbesets, dp = dp)
       }

