Description Usage Arguments Extends Creating Objects Slots Methods Author(s) See Also Examples
Container for high-throughput assays and experimental
metadata. ExpressionSet
class is derived from
eSet
, and requires a matrix named exprs
as
assayData member.
1 2 3 4 5 6 7 8 9 | ## 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
|
assayData |
A When When |
phenoData |
An optional |
featureData |
An optional |
experimentData |
An optional |
annotation |
A |
protocolData |
An optional |
... |
Additional arguments, passed to
|
Directly extends class eSet
.
ExpressionSet
instances are usually created through
ExpressionSet()
.
Inherited from eSet
:
assayData
:Contains matrices with equal
dimensions, and with column number equal to
nrow(phenoData)
. assayData
must contain a matrix
exprs
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 in assayData
. Class:AssayData-class
phenoData
:See eSet
featureData
:See eSet
experimentData
:See eSet
annotation
:See eSet
protocolData
:See eSet
Class-specific methods.
as(exprSet,"ExpressionSet")
Coerce objects of
exprSet-class
to ExpressionSet
as(object,"data.frame")
Coerce objects of
ExpressionSet-class
to data.frame
by
transposing the expression matrix and concatenating phenoData
exprs(ExpressionSet)
, exprs(ExpressionSet,matrix)<-
Access and
set elements named exprs
in the AssayData-class
slot.
esApply(ExpressionSet, MARGIN, FUN,
...)
'apply'-like function to conveniently operate on
ExpressionSet
objects. See esApply
.
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
and eSet
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)
and sampleNames(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. See
updateObject
, Versions-class
.
validObject(ExpressionSet)
:Validity-checking method, ensuring
that exprs
is a member of
assayData
. checkValidity(ExpressionSet)
imposes this
validity check, and the validity checks of eSet
.
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
to ExpressionSet
.
as(eSet,ExpressionSet)
:Coerce the eSet
portion of an object to ExpressionSet
.
show(ExpressionSet)
See eSet
dim(ExpressionSet)
, ncol
See eSet
ExpressionSet[(index)
:See eSet
ExpressionSet$
, ExpressionSet$<-
See eSet
ExpressionSet[[i]]
, ExpressionSet[[i]]<-
See eSet
Biocore team
eSet-class
, ExpressionSet-class
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | # create an instance of ExpressionSet
ExpressionSet()
ExpressionSet(assayData=matrix(runif(1000), nrow=100, ncol=10))
# update an existing ExpressionSet
data(sample.ExpressionSet)
updateObject(sample.ExpressionSet)
# information about assay and sample data
featureNames(sample.ExpressionSet)[1:10]
sampleNames(sample.ExpressionSet)[1:5]
experimentData(sample.ExpressionSet)
# subset: first 10 genes, samples 2, 4, and 10
expressionSet <- sample.ExpressionSet[1:10,c(2,4,10)]
# named features and their expression levels
subset <- expressionSet[c("AFFX-BioC-3_at","AFFX-BioDn-5_at"),]
exprs(subset)
# samples with above-average 'score' in phenoData
highScores <- expressionSet$score > mean(expressionSet$score)
expressionSet[,highScores]
# (automatically) coerce to data.frame
lm(score~AFFX.BioDn.5_at + AFFX.BioC.3_at, data=subset)
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