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

#createTargetsFile(verbose=T)