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]