makeGenericArray        package:GenomeGraphs        R Documentation

_C_r_e_a_t_e_s _a_n _o_b_j_e_c_t _o_f _c_l_a_s_s _G_e_n_e_r_i_c_A_r_r_a_y

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

     Creates an object of class Generic Array representing microarray
     data.  This could be gene expression, array CGH, etc.

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

     makeGenericArray(intensity, probeStart, probeEnd, segmentation, dp = NULL)

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

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

probeStart: Vector of start positions for the probes

probeEnd: Vector of end positions for probes (optional)

segmentation: Object of class Segmentation, needs to be added if
          segments should be plotted as well

      dp: Object of class DisplayPars which handles the display
          parameters for plotting

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

     Object of class GenericArray

_W_a_r_n_i_n_g:

     ....

_N_o_t_e:

     ~~further notes~~ 

     ~Make other sections like Warning with \section{Warning }{....} ~

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

     Jim Bullard and Steffen Durinck

_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:

     ~~objects to See Also as 'help', ~~~

_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, segmentation, dp = NULL) 
     {
         pt <- getClass("GenericArray")@prototype
         if (is.null(dp)) 
             dp <- pt@dp
         if (missing(probeEnd)) 
             probeEnd <- pt@probeEnd
         if (missing(segmentation)) 
             segmentation <- pt@segmentation
         if (missing(probeStart)) 
             stop("Need probeStart argument to know where to plot the data on the genome")
         new("GenericArray", intensity = intensity, probeStart = probeStart, 
             probeEnd = probeEnd, dp = dp, segmentation = segmentation)
       }

