readBeadSummaryData {beadarray} | R Documentation

## Read bead summary data information into R

### Description

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.

### Usage

    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)

### Arguments

`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.

### Details

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_ARRAYNend{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.

### Value

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

### Author(s)

Mark Dunning and Mike Smith

### See Also

`BeadSummaryList` `readBeadSummaryTargets`

### Examples

    #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")

[Package beadarray version 1.0.0 Index]