oligo (version 1.36.1)

read.xysfiles: Parser to XYS files

Description

NimbleGen provides XYS files which are read by this function.

Usage

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)

Arguments

...

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.

Value

• ExpressionFeatureSet
  if Expresssion arrays
• TilingFeatureSet
  if Tiling arrays

Details

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.

See Also

list.xysfiles, read.celfiles

Examples

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)
}