readBeadSummaryOutput: Read bead-summary intensities from two colour Illumina...
In beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

Description Usage Arguments Details Value Author(s) References See Also Examples

Reads text-files with bead summary output for each array and arranges the data in a "BeadSetIllumina" object

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readBeadSummaryOutput(arrayNames = NULL, path = ".",
    pattern = "beadTypeFile.txt", recursive = FALSE, sep = ",",
    fullPaths = NULL, sepchar = "_", prList = NULL)

`arrayNames`	Character vector containing names of arrays to be read. If `fullPaths` is specified, `arrayNames` searches only among these, otherwise it searches in current working directory. More commonly `arrayNames` is `NULL`, then all arrays in current working directory or as specified in `fullPaths` are read
`path`	Character string specifying the data-directory
`pattern`	Character string specifying the file-name ending of the files to be read
`recursive`	If `fullPaths` is not specified, the logical `recursive` regulates whether or not the function should look for files recursively
`sep`	Delimiter in text-files
`fullPaths`	Character vector containing the names of the files of interest, including the directories in which they are found (from the working directory `path`). Typically on a form similar to `<chip>/<chip>_<row>_<pattern>`. Useful when the current directory contains arrays from several experiments/families, and only a subset is to be loaded at the time. Usually used in combination with `arrayNames=NULL`
`sepchar`	Character used to bind togeher different parts of the file-names (“_” in the above example)
`prList`	Character vector with Illumina probe-IDs. Should be specified in the rare case that different arrays contain different probes.

The scanner protocol must be set to save bead-summary data. The function expects the following data-fields in each file: “Illumicode”, “N”, “Mean GRN”, “Dev GRN”, “Mean RED”, “Dev RED” (in that order). The first two are the bead-type ID and the number of detected beads. The rest contain a robust bead-type mean and the standard deviation of the signal for each channel.

The probes found in the first loaded array define prList unless otherwise specified. A warning is issued if additional probes are found in a subsequent array. It is an error if not all markers in prList are found in subsequent arrays.

Much of the functionality is adapted from the beadarray package (Dunning et al., 2007). This package is an excellent resource for loading and analysing raw Illumina BeadArray data, including images.

"BeadSetIllumina" object, with the assayData entries

`R`	Mean red signal (`"Mean RED"`)
`se.R`	Standard error of the mean red signal (`"Dev RED"/sqrt("N")`)
`G`	Mean green signal (`"Mean GRN"`)
`se.G`	Standard error of the mean green signal (`"Dev GRN"/sqrt("N")`)
`no.beads`	Number of detected beads

Lars Gidskehaug

M. J. Dunning et al. (2007) beadarray: R classes and methods for Illumina bead-based data. Bioinformatics 23(16):2183-4

BeadSetIllumina, scatterArrays, preprocessBeadSet, createAlleleSet

## Not run: 
#Read a BeadSetIllumina object using files in example data directory
rPath <- system.file("extdata", package="beadarrayMSV")
BSDataRaw <- readBeadSummaryOutput(path=rPath,recursive=TRUE)

#Print information from object
BSDataRaw
pData(BSDataRaw)
varMetadata(BSDataRaw)

#Alternatively:
sampleFile <- paste(rPath,'sampleData.txt',sep='/')
sampleInfo <- read.table(sampleFile,skip=8,sep='\t',header=TRUE,
    colClasses='character')
rownames(sampleInfo) <- make.names(paste(sampleInfo$chip,
    sampleInfo$row,sep='_'))
pattern <- 'beadTypeFile.txt'
fullPaths <- paste(sampleInfo$chip,'/',sampleInfo$chip,'_',
    sampleInfo$row,'_',pattern,sep='')
BSDataRaw <- readBeadSummaryOutput(fullPaths=fullPaths[1:4],
    path=rPath,pattern=pattern)

## Plot G vs. R
dev.new()
scatterArrays(BSDataRaw,smooth=FALSE)

## End(Not run)