createTargetsFile: A function to generate a targets file given a directory of...

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

View source: R/createTargetsFile.R

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

1
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.

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

1
#createTargetsFile(verbose=T)

beadarray documentation built on Nov. 17, 2017, 11:36 a.m.