createTargetsFile {beadarray} | R Documentation |
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.
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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.
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channel1 |
channel1 : The string indicating that files are associated with the first channel (usually Grn).
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channel2 |
channel2 : The string indicating that files are associated with the second channel (usually Red).
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txtsuff |
txtsuff : The suffix of files containing the bead-level intensities (usually txt, but occasionally csv).
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imgsuff |
imgsuff : The suffix of files containing the images.
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locssuff |
locssuff : The suffix of files containing the precise bead locations (usually locs).
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xmlsuff |
xmlsuff : The suffix of files containing the meta-data (usually xml).
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verbose |
verbose : Determines whether or not the function reports on its progress as it goes along.
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special |
special : Files with names containing special words (such as fiducial) are ignored.
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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.
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metricsflag |
codemetricsflag: This gives the key word that can be used to identify metrics files.
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metsep |
metsep : This gives the cell separator used in the metrics file.
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metricsection |
metricsection : This gives the column heading used in the metrics file to indicate array section names.
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metricchip |
metricchip : This gives the column heading used in the metrics file to indicate the chip name.
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Details
This function bases its resultant targets file on the files with suffix txtsuff.
Value
This returns a dataframe containing
Author(s)
Andy Lynch
See Also
readIlluminaData()
Examples
#createTargetsFile(verbose=T)
[Package
beadarray version 2.34.0
Index]