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beadarray (version 2.22.2)

createTargetsFile: A function to generate a targets file given a directory of Illumina bead-level files

Description

This function, when pointed to a directory containing Illumina bead-level files (e.g. txt, idat, locs, tif) will return a simple targets file of the sort expected by beadarray. Note that a user created targets file is likely to be of greater value.

Usage

createTargetsFile(dir = NULL, nochannels = 1, channel1 = "Grn", channel2 = "Red", txtsuff = "txt", imgsuff = "tif", locssuff = "locs", xmlsuff = "xml", verbose = FALSE, special = c("sdf", "fiducial"), ColourConfusionStop = T, metricsflag = "Metrics", metsep = "\t", metricsection = "Section", metricchip = "Matrix")

Arguments

dir
dir: The directory containing the Illumina bead-level files. By default, will search the working directory.
nochannels
nochannels: Does the directory contain 1 or 2 channel arrays? Setting this argument to be null will result in the function making its best guess.
channel1
channel1: The string indicating that files are associated with the first channel (usually Grn).
channel2
channel2: The string indicating that files are associated with the second channel (usually Red).
txtsuff
txtsuff: The suffix of files containing the bead-level intensities (usually txt, but occasionally csv).
imgsuff
imgsuff: The suffix of files containing the images.
locssuff
locssuff: The suffix of files containing the precise bead locations (usually locs).
xmlsuff
xmlsuff: The suffix of files containing the meta-data (usually xml).
verbose
verbose: Determines whether or not the function reports on its progress as it goes along.
special
special: Files with names containing special words (such as fiducial) are ignored.
ColourConfusionStop
ColourConfusionStop: This determines the behaviour of the function if there is a discrepancy between the number of channels specified, and the number apparently present.
metricsflag
codemetricsflag: This gives the key word that can be used to identify metrics files.
metsep
metsep: This gives the cell separator used in the metrics file.
metricsection
metricsection: This gives the column heading used in the metrics file to indicate array section names.
metricchip
metricchip: This gives the column heading used in the metrics file to indicate the chip name.

Value

This returns a dataframe containing

Details

This function bases its resultant targets file on the files with suffix txtsuff.

See Also

readIlluminaData()

Examples

Run this code

#createTargetsFile(verbose=T)

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