eSet {Biobase}R Documentation

General Container for High-Throughput Assays and Experimental Metadata

Description

General container for high-throughput assays and experimental metadata. eSet class is derived from annotatedDataset class.

Extends

Directly extends class annotatedDataset.

Objects from the Class

Objects can be created by calls of the form new("eSet", ...).

Slots

Derived from annotatedDataset:

reporterInfo
class:data.frameOrNULL
phenoData
class:phenoData

Introduced in eSet:

assayData:
Can be a list of matrices or an environment populated by matrices. The matrices must have common dimensions, and number of columns must agree with number of rows of phenoData pData slot; class:listOrEnv
sampleNames:
Vector of sample names, class:character
reporterNames:
Vector of reporter names, class:character
description:
Vector of reporter names, class:characterORMIAME
notes:
Notes, class:character
annotation:
Annotation, class:character
history:
History, class:character

Methods

Derived from annotatedDataset:

$(eSet) and $(eSet, value)<-
see annotatedDataset
phenoData(eSet) and phenoData(eSet, value)<-
see annotatedDataset
reporterInfo(eSet) and reporterInfo(eSet, value)<-
see annotatedDataset
pData(eSet) and pData(eSet, value)<-
see annotatedDataset
[[(index) and [[(index, value)<-:
see annotatedDataset
varLabels(eSet)
see annotatedDataset

Class-specific methods:

assayData(eSet) and assayData(eSet, listOrEnc)<-:
Access/set eSet data.
exprs(eSet) and exprs(eSet)<-:
Not documented
description(eSet) and description(eSet, value)<-:
Not documented
annotation(eSet) and annotation(eSet, value)<-:
Not documented
notes(eSet) and notes(eSet, value)<-:
Not documented
sampleNames(eSet) and sampleNames(eSet, value)<-:
Not documented
reporterNames(eSet) and reporterNames(eSet, value)<-:
Not documented
combine(eSet, eSet):
Not documented
getExpData(eSet, character):
DEPRECATED
eList(eSet) and eList(eSet, value)<-:
DEPRECATED

Standard generic methods:

[(index):
Conducts subsetting of matrices and phenoData components
dim(eSet):
Not documented
ncol(eSet):
Not documented
show(eSet):
Not documented

Note

Class listOrEnv is a (virtual) class union.

golubMergeSub is an exprSet example that can be coerced to eSet; see the eSet vignette.

Author(s)

V.J. Carey, after initial design by R. Gentleman

See Also

annotatedDataset, phenoData, exprSet

Examples

# eSet 1 is loaded
data(eset)
pd <- phenoData(eset)
xl <- list(e1=exprs(eset))
gn <- geneNames(eset)
sn <- sampleNames(eset)

# eSet 2 is constructed
es2 <- new("eSet", phenoData=pd, assayData=xl,
  reporterNames=gn, sampleNames=sn)

# illustrate subset and show for assayData as list
es2[1:4,1:4]

# build with environment assayData
eenv <- new.env()
assign("e1", assayData(eset), eenv)
es3 <- new("eSet", phenoData=pd, assayData=eenv,
  reporterNames=gn, sampleNames=sn)
es3
es3[1:5,1:5]

# show some legacy behavior: set list element name to
# exprs and invoke exprs()
names(assayData(es2)) <- "exprs"
dim(exprs(es2))

# show some validity checking
assayData(es3) <- assayData(es2)
es3  # now has list
sampleNames(es2) <- letters # ok
if (interactive()) {
 lk <- try(sampleNames(es2) <- letters[-1]) # not ok
 lk
 lk <- try(assayData(es2) <- assayData(es2[-1,])) # not ok
 class(lk)
 }

# work with the swirl data
data(SW)
data(swrep)
data(SWPD)
sw <- new("eSet",
  assayData=list( R=SW$R, G=SW$G, Rb=SW$Rb, Gb=SW$Gb),
  phenoData=SWPD, reporterInfo=swrep, sampleNames=as.character(1:4),
  reporterNames=as.character(swrep$Name))

[Package Biobase version 1.8.0 Index]