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")
dir
: The directory containing the Illumina bead-level files. By default, will search the working directory.
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
: The string indicating that files are associated with the first channel (usually Grn).
channel2
: The string indicating that files are associated with the second channel (usually Red).
txtsuff
: The suffix of files containing the bead-level intensities (usually txt, but occasionally csv).
imgsuff
: The suffix of files containing the images.
locssuff
: The suffix of files containing the precise bead locations (usually locs).
xmlsuff
: The suffix of files containing the meta-data (usually xml).
verbose
: Determines whether or not the function reports on its progress as it goes along.
special
: Files with names containing special words (such as fiducial) are ignored.
ColourConfusionStop
: This determines the behaviour of the function if there is a discrepancy between the number of channels specified, and the number apparently present.
metsep
: This gives the cell separator used in the metrics file.
metricsection
: This gives the column heading used in the metrics file to indicate array section names.
metricchip
: This gives the column heading used in the metrics file to indicate the chip name.
#createTargetsFile(verbose=T)
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