readBeadSummaryData        package:beadarray        R Documentation

_R_e_a_d _b_e_a_d _s_u_m_m_a_r_y _d_a_t_a _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:

     Function to read pre-processed bead summary data into R. Data can
     be the output from BeadStudio with either a separate file for each
     array in the experiment, or each file containing all arrays on a
     SAM.

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

     readBeadSummaryData(targets=NULL, header=T, sep=",",path=NULL,
                                        columns = list(ProbeID = "TargetID",
                                          AvgSig = "AVG_Signal", Nobeads = "Avg_NBEADS",
                                          Detection="Detection", BeadStDev="BEAD_STDEV"),
                                        other.columns = NULL, skip=7)

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

 targets: either a list of files created by readBeadSummaryTargets or 
          NULL to read all files in a directory.

     sep: character used to seperate each column in the file. Usually
          either "," or "\t".

 columns: list defining the names for each column to be read from the
          input files

other.columns: list defining any additional columns to be read from the
          input.

  header: if TRUE then function will read column headers from the input
          files.

    path: optional argument to specify the location of the data to be
          read. By default, files are read from the current working
          directory.

    skip: number of lines to ignore when reading the input files.

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

     This function can be used to read the standard output from the
     Illumina BeadStudio application with default column names for
     Average Signal, Bead Stdev, Number of Beads and Detection and in
     the Column-oriented (Comma delimited) file format. ie the number
     of rows in each file is the number of bead types in the experiment
     and columns are repeated such that each row describes the
     information for each array in the experiment. The files are
     assumed to contain header information created by Illumina and this
     is skipped when the files are read. The skip parameter can be
     adjusted accordingly for files with a non-standard amount of
     header information.

     The names specified in the columns parameter are used to read the
     file. It is assumed that the average bead intensities for each
     array appear in columns with headings of the form
     \begin{verbatim}AVG_Signal_ARRAY1,
     AVG_Signal_ARRAY2....AVG_Signal_ARRAYN\end{verbatim} for the N
     arrays found in the file. All other columns headings are found in
     the same way.

     A separate BeadSummaryList object (described below) is created for
     each file listed in the targets object.

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

     An BeadSummaryList object containing the components

     R data frame containing the averaged foreground intensities for
     each bead type for each array after outlier removal BeadStDev data
     frame containing the standard deviation for each bead type for
     each array NoBeads data frame containing the number of beads used
     to calculate the average for each bead type Detection data frame
     containing the average detection score for each bead type for each
     array other   data frame containing matrices corresponding to
     other.columns if given

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

     Mark Dunning and Mike Smith

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

     'BeadSummaryList' 'readBeadSummaryTargets'

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

     #To read all bead summary files in current directory simply use
     #
     #BSData = readBeadSummaryData()
     #
     #if the files are contained in subdirectory New Folder
     #BSData = readBeadSummaryData(path="New Folder")
     #
     #if all header information has been removed...
     #BSData = readBeadSummaryData(skip=0)
     #
     #
     #targets=readBeadSummaryTargets("targets.txt")
     #
     #BSData=readBeadSummaryData(targets)
     #
     #
     #to also read the MAX_Signal column for each array 
     #
     #BSData = readBeadSummaryData(other.columns="MAX_Signal")

