ExpressionSet {Biobase} | R Documentation |
Class to Contain and Describe High-Throughput Expression Level Assays.
Description
Container for high-throughput assays and experimental
metadata. ExpressionSet
class is derived from
eSet
, and requires a matrix named exprs
as
assayData member.
Usage
## Instance creation
ExpressionSet(assayData,
phenoData=annotatedDataFrameFrom(assayData, byrow=FALSE),
featureData=annotatedDataFrameFrom(assayData, byrow=TRUE),
experimentData=MIAME(), annotation=character(),
protocolData=annotatedDataFrameFrom(assayData, byrow=FALSE),
...)
## Additional methods documented below
Arguments
assayData |
A When When |
phenoData |
An optional |
featureData |
An optional |
experimentData |
An optional |
annotation |
A |
protocolData |
An optional |
... |
Additional arguments, passed to
|
Extends
Directly extends class eSet
.
Creating Objects
ExpressionSet
instances are usually created through
ExpressionSet()
.
Slots
Inherited from eSet
:
assayData
:Contains matrices with equal dimensions, and with column number equal to
nrow(phenoData)
.assayData
must contain a matrixexprs
with rows representing features (e.g., probe sets) and columns representing samples. Additional matrices of identical size (e.g., representing measurement errors) may also be included inassayData
. Class:AssayData-class
phenoData
:See
eSet
featureData
:See
eSet
experimentData
:See
eSet
annotation
:See
eSet
protocolData
:See
eSet
Methods
Class-specific methods.
as(exprSet,"ExpressionSet")
Coerce objects of
exprSet-class
toExpressionSet
as(object,"data.frame")
Coerce objects of
ExpressionSet-class
todata.frame
by transposing the expression matrix and concatenatingphenoData
exprs(ExpressionSet)
,exprs(ExpressionSet,matrix)<-
Access and set elements named
exprs
in theAssayData-class
slot.esApply(ExpressionSet, MARGIN, FUN, ...)
'apply'-like function to conveniently operate on
ExpressionSet
objects. SeeesApply
.write.exprs(ExpressionSet)
Write expression values to a text file. It takes the same arguments as
write.table
Derived from eSet
:
updateObject(object, ..., verbose=FALSE)
Update instance to current version, if necessary. See
updateObject
andeSet
isCurrent(object)
Determine whether version of object is current. See
isCurrent
isVersioned(object)
Determine whether object contains a 'version' string describing its structure . See
isVersioned
assayData(ExpressionSet)
:See
eSet
sampleNames(ExpressionSet)
andsampleNames(ExpressionSet)<-
:See
eSet
featureNames(ExpressionSet)
,featureNames(ExpressionSet, value)<-
:See
eSet
dims(ExpressionSet)
:See
eSet
phenoData(ExpressionSet)
,phenoData(ExpressionSet,value)<-
:See
eSet
varLabels(ExpressionSet)
,varLabels(ExpressionSet, value)<-
:See
eSet
varMetadata(ExpressionSet)
,varMetadata(ExpressionSet,value)<-
:See
eSet
pData(ExpressionSet)
,pData(ExpressionSet,value)<-
:See
eSet
varMetadata(ExpressionSet)
,varMetadata(ExpressionSet,value)
See
eSet
experimentData(ExpressionSet)
,experimentData(ExpressionSet,value)<-
:See
eSet
pubMedIds(ExpressionSet)
,pubMedIds(ExpressionSet,value)
See
eSet
abstract(ExpressionSet)
:See
eSet
annotation(ExpressionSet)
,annotation(ExpressionSet,value)<-
See
eSet
protocolData(ExpressionSet)
,protocolData(ExpressionSet,value)<-
See
eSet
combine(ExpressionSet,ExpressionSet)
:See
eSet
storageMode(ExpressionSet)
,storageMode(ExpressionSet,character)<-
:See
eSet
Standard generic methods:
initialize(ExpressionSet)
:Object instantiation, used by
new
; not to be called directly by the user.updateObject(ExpressionSet)
:Update outdated versions of
ExpressionSet
to their current definition. SeeupdateObject
,Versions-class
.validObject(ExpressionSet)
:Validity-checking method, ensuring that
exprs
is a member ofassayData
.checkValidity(ExpressionSet)
imposes this validity check, and the validity checks ofeSet
.makeDataPackage(object, author, email, packageName, packageVersion, license, biocViews, filePath, description=paste(abstract(object), collapse="\n\n"), ...)
-
Create a data package based on an ExpressionSet object. See
makeDataPackage
. as(exprSet,ExpressionSet)
:Coerce
exprSet
toExpressionSet
.as(eSet,ExpressionSet)
:Coerce the
eSet
portion of an object toExpressionSet
.show(ExpressionSet)
See
eSet
dim(ExpressionSet)
,ncol
See
eSet
ExpressionSet[(index)
:See
eSet
ExpressionSet$
,ExpressionSet$<-
See
eSet
ExpressionSet[[i]]
,ExpressionSet[[i]]<-
See
eSet
Author(s)
Biocore team
See Also
eSet-class
, ExpressionSet-class
.
Examples
# create an instance of ExpressionSet
ExpressionSet()
ExpressionSet(assayData=matrix(runif(1000), nrow=100, ncol=10))
# update an existing ExpressionSet
data(sample.ExpressionSet)
updateObject(sample.ExpressionSet)
# information about assay and sample data
featureNames(sample.ExpressionSet)[1:10]
sampleNames(sample.ExpressionSet)[1:5]
experimentData(sample.ExpressionSet)
# subset: first 10 genes, samples 2, 4, and 10
expressionSet <- sample.ExpressionSet[1:10,c(2,4,10)]
# named features and their expression levels
subset <- expressionSet[c("AFFX-BioC-3_at","AFFX-BioDn-5_at"),]
exprs(subset)
# samples with above-average 'score' in phenoData
highScores <- expressionSet$score > mean(expressionSet$score)
expressionSet[,highScores]
# (automatically) coerce to data.frame
lm(score~AFFX.BioDn.5_at + AFFX.BioC.3_at, data=subset)