read.xysfiles {oligo}R Documentation

Parser to XYS files

Description

NimbleGen provides XYS files which are read by this function.

Usage

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

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

Arguments

... file names
filenames character vector with filenames.
channel1 a character vector with the CEL filenames for the first 'channel' on a Tiling application
channel2 a character vector with the CEL filenames for the second 'channel' on a Tiling application
pkgname character vector with alternative PD Info package name
phenoData phenoData
featureData featureData
experimentData experimentData
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.

Details

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

Value

ExpressionFeatureSet if Expresssion arrays
TilingFeatureSet if Tiling arrays

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)
}

[Package oligo version 1.8.3 Index]