read.xysfiles {oligo} | R Documentation |
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 |
|
channel1 |
a |
channel2 |
a |
pkgname |
|
phenoData |
|
featureData |
|
experimentData |
|
protocolData |
|
notes |
|
verbose |
|
sampleNames |
|
checkType |
|
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.
|
if Expresssion arrays |
|
if Tiling arrays |
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) }