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
:Contains matrices with equal dimensions,
and with column number equal to
nrow(phenoData)
. assayData
must contain a matrix
exprs
and a matrix spikeIn
with rows representing
features and columns representing samples.
phenoData
:See eSet
annotation
See eSet
featureData
See eSet
experimentData
:See eSet
Class-specific methods:
spikeIn(SpikeInExpressionSet)
,
spikeIn(SpikeInExpressionSet)<-
Access and set elements
named spikeIn
in the AssayData-class
slot.
spkSplit(SpikeInExpressionSet)
creates two SpikeInExpressionSet objects – one with the spike-in probes and one with the non-spike-in probes.
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)