Learn R Programming

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

  • ExpressionFeatureSetif Expresssion arrays
  • TilingFeatureSetif 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

Run this code
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)
}

Run the code above in your browser using DataLab