| SpikeInExpressionSet-class {spkTools} | R Documentation |
This is a class representation for spike-in expression
data. SpikeInExpressionSet class is derived from
ExpressionSet, and requires a matrix names exprs
and a matrix named spikeIn.
Extends class ExpressionSet.
createSpikeInExpressionSet(exprs, spikeIn, ...)
new("SpikeInExpressionSet",
phenoData = new("AnnotatedDataFrame"),
featureData = new("AnnotatedDataFrame"),
experimentData = new("MIAME"),
annotation = character(0),
exprs = new("matrix"),
spikeIn = new("matrix"))
This creates a SpikeInExpressionSet with assayData
implicitly created to contain exprs and
spikeIn. Additional named matrix arguments with the same
dimensions as exprs are added to assayData; the row
and column names of these additional matrices should match those of
exprs and spikeIn.
new("SpikeInExpressionSet",
assayData = assayDataNew(exprs=new("matrix"),spikeIn=new("matrix")),
phenoData = new("AnnotatedDataFrame"),
featureData = new("AnnotatedDataFrame"),
experimentData = new("MIAME"),
annotation = character(0),
This creates a SpikeInExpressionSet with assayData
provided explicitly. In this form, the only required named argument is
assayData.
Inherited from ExpressionSet:
assayData:nrow(phenoData). assayData must contain a matrix
exprs and a matrix spikeIn with rows representing
features and columns representing samples.phenoData:eSetannotationeSetfeatureDataeSetexperimentData:eSetClass-specific methods:
spikeIn(SpikeInExpressionSet),
spikeIn(SpikeInExpressionSet)<-spikeIn in the AssayData-class slot.spkSplit(SpikeInExpressionSet)
For derived methods (see ExpressionSet).
eSet-class, ExpressionSet-class.
# create an instance of SpikeInExpressionSet
new("SpikeInExpressionSet")
new("SpikeInExpressionSet", exprs=matrix(runif(1000), nrow=100), spikeIn=matrix(rep(1:10,100), nrow=100))
# class specific methods
data(affy)
affySpikes <- spikeIn(affy)
affySplit <- spkSplit(affy)