read.xysfiles: Parser to XYS files
In benilton/oligo-release: Preprocessing tools for oligonucleotide arrays.

Description Usage Arguments Details Value See Also Examples

NimbleGen provides XYS files which are read by this function.

read.xysfiles(..., filenames, pkgname, phenoData, featureData,
experimentData, protocolData, notes, verbose=TRUE, sampleNames,
checkType=TRUE)

read.xysfiles2(channel1, channel2, pkgname, phenoData, featureData,
experimentData, protocolData, notes, verbose=TRUE, sampleNames,
checkType=TRUE)

`...`	file names
`filenames`	`character` vector with filenames.
`channel1`	a `character` vector with the XYS filenames for the first 'channel' on a Tiling application
`channel2`	a `character` vector with the XYS filenames for the second 'channel' on a Tiling application
`pkgname`	`character` vector with alternative PD Info package name
`phenoData`	`phenoData`
`featureData`	`featureData`
`experimentData`	`experimentData`
`protocolData`	`protocolData`
`notes`	`notes`
`verbose`	`verbose`
`sampleNames`	`character` vector with sample names (usually better descriptors than the filenames)
`checkType`	`logical`. Check type of each file? This can be time consuming.

The function will read the XYS files provided by NimbleGen Systems and return an object of class FeatureSet.

The function guesses which annotation package to use from the header of the XYS file. The user can also provide the name of the annotaion package to be used (via the pkgname argument). If the annotation package cannot be loaded, the function returns an error. If the annotation package is not available from BioConductor, one can use the pdInfoBuilder package to build one.

`ExpressionFeatureSet`	if Expresssion arrays
`TilingFeatureSet`	if Tiling arrays

list.xysfiles, read.celfiles

if (require(maqcExpression4plex) & require(pd.hg18.60mer.expr)){
xysPath <- system.file("extdata", package="maqcExpression4plex")
xysFiles <- list.xysfiles(xysPath, full.name=TRUE)
ngsExpressionFeatureSet <- read.xysfiles(xysFiles)
}