Description Extends Creating Objects Slots Methods See Also Examples
This is a class representation for fRMA-preprocessed expression
data. frmaExpressionSet
class is derived from
ExpressionSet
, and requires a matrix named exprs
and optionally matrices named se.exprs
, weights
, and residuals
.
Extends class ExpressionSet
.
new("frmaExpressionSet",
exprs = new("matrix"),
se.exprs = new("matrix"),
weights=new("matrix"),
residuals=new("matrix"),
randomeffects=new("matrix"),
phenoData = new("AnnotatedDataFrame"),
featureData = new("AnnotatedDataFrame"),
experimentData = new("MIAME"),
annotation = new("character"),
...)
This creates a frmaExpressionSet
with assayData
implicitly created to contain exprs
and se.exprs
. The
only required named arguments is exprs
. Three optional named
matrices, weights
, residuals
, and randomeffects
can be added to the object.
new("frmaExpressionSet",
assayData = assayDataNew(exprs=new("matrix"),se.exprs=new("matrix")),
weights=new("matrix"),
residuals=new("matrix"),
randomeffects=new("matrix"),
phenoData = new("AnnotatedDataFrame"),
featureData = new("AnnotatedDataFrame"),
experimentData = new("MIAME"),
annotation = new("character"),
...)
This creates a frmaExpressionSet
with assayData
provided
explicitly. In this form, the only required named argument is
assayData
. Three optional named matrices, weights
,
residuals
, and randomeffects
can be added to the object.
se.exprs
:standard errors for the expression estimates
weights
:weights used in the summarization step
residuals
:residuals from fitting the probe-level model
randomeffects
:random effect estimates from fitting the probe-level model using random effect summarization
Inherited from ExpressionSet
:
assayData
:Contains matrices with equal dimensions,
and with column number equal to
nrow(phenoData)
. assayData
must contain a matrix
exprs
with rows representing features and columns
representing samples. It may also contain a matrix se.exprs
containing standard errors.
phenoData
:See eSet
annotation
:See eSet
featureData
:See eSet
experimentData
:See eSet
Class-specific methods:
se.exprs(frmaExpressionSet)
Access elements named
se.exprs
in the AssayData-class
slot.
weights(frmaExpressionSet)
Access elements named
weights
residuals(frmaExpressionSet)
Access elements named
residuals
randomeffects(frmaExpressionSet)
Access elements named
randomeffects
For derived methods (see ExpressionSet
).
eSet-class
, ExpressionSet-class
, frma
.
1 2 | # create an instance of frmaExpressionSet
new("frmaExpressionSet")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.