readBeadImages           package:beadarray           R Documentation

_R_e_a_d _B_e_a_d_A_r_r_a_y _i_n_f_o_r_m_a_t_i_o_n _i_n_t_o _R

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

     Uses image and csv files to load information about each array used
     in the experiment.

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

     readBeadImages(targets, path=NULL, sharpen=TRUE, backgroundSize=17, columns=list(ProbeID="Code", x="x", y="y"),numrow=NULL)

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

 targets: targets vector which defines the images and csv files used to
          read each array

    path: character string specifying the location of files to be read
          by the function

 sharpen: if TRUE then the Illumina sharpening mask will be used prior
          to foreground averages being calculated

backgroundSize: numeric value which defines the size of the n x n box
          we will use to calculate local background values

 columns: vector specifying the column headings to be read from the csv
          files

  numrow: used to specify the number of rows (ie beads) each input file
          will contain. If specified in advance this can speed the 
          reading of the data.

_D_e_t_a_i_l_s:

     The targets objects can be read in previously by using a
     'read.table' command. This defines the location of the csv and pgm
     files that are required. The column headings Image1 and xyInfo
     must be found in the targets object. csv files are used to specify
     the location and identity of each bead on the array and must
     contain columns for  the $x$ and $y$ postion of each bead as well
     as a ProbeID. The names of these columns can be specified by
     setting the 'columns' parameter

     The foreground and background intensities of each bead are then
     calculated and stored separately. For foreground calculations the
     sharpening mask used by Illumina  is used prior to an averaging
     over the 9 pixels in a 3 x 3 square closest to the bead centre (we
     can choose to calculate the values obtained without this mask).
     For  the background intensity we look at the pixels in a 17 x 17
     square and calculate the mean of the 5 lowest values inside this
     square.  If a bead is particularly close to the edge of the image
     then it isn't possible to take a 17 x 17 square for sampling.  In
     this case the background value is taken as the mean of all the
     previous background values and the user is informed that this has
     been done.

     The function creates an BeadLevelList containing foreground,
     background intensities for each bead on each array

     Function requires the 'pixmap' library to be loaded

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

     BeadLevelList object with list components R, Rb, G, Gb

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

     Mark Dunning, Mike Smith

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

     #library(pixmap)

     #targets = read.table("targets.txt", header=T)

     #targets

     #May take a while to run

     #BLData.s = readBeadImages(targets)

     #Create foreground intensities without using sharpening. Should take less time
     #BLData.ns = readBeadImages(targets, sharpen=FALSE)

     #Use a 9 x 9 are around each bead to calculate the background

     #BLData.ns.9 = readBeadImages(targets, sharpen=FALSE, backgroundSize=9)

