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.
`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

    #createTargetsFile(verbose=T)

[Package beadarray version 2.36.1 Index]