| eSet {Biobase} | R Documentation |
General container for high-throughput assays and experimental metadata. eSet class is derived from annotatedDataset class.
Directly extends class annotatedDataset.
Objects can be created by calls of the form new("eSet", ...).
Derived from annotatedDataset:
reporterInfodata.frameOrNULLphenoDataphenoData
Introduced in eSet:
assayData:phenoData pData slot; class:listOrEnvsampleNames:characterreporterNames:characterdescription:class:characterORMIAMEnotes:characterannotation:characterhistory:character
Derived from annotatedDataset:
$(eSet) and $(eSet, value)<-annotatedDatasetphenoData(eSet) and phenoData(eSet, value)<-annotatedDatasetreporterInfo(eSet) and reporterInfo(eSet, value)<-annotatedDatasetpData(eSet) and pData(eSet, value)<-annotatedDataset[[(index) and [[(index, value)<-:annotatedDatasetvarLabels(eSet)annotatedDatasetClass-specific methods:
assayData(eSet) and assayData(eSet, listOrEnc)<-:eSet data.exprs(eSet) and exprs(eSet)<-:description(eSet) and description(eSet, value)<-:annotation(eSet) and annotation(eSet, value)<-:notes(eSet) and notes(eSet, value)<-:sampleNames(eSet) and sampleNames(eSet, value)<-:reporterNames(eSet) and reporterNames(eSet, value)<-:combine(eSet, eSet):getExpData(eSet, character):eList(eSet) and eList(eSet, value)<-:Standard generic methods:
[(index):dim(eSet):ncol(eSet):show(eSet):
Class listOrEnv is a (virtual) class union.
golubMergeSub is an exprSet example that can be coerced to eSet; see the eSet vignette.
V.J. Carey, after initial design by R. Gentleman
annotatedDataset, phenoData, exprSet
# eSet 1 is loaded
data(eset)
pd <- phenoData(eset)
xl <- list(e1=exprs(eset))
gn <- geneNames(eset)
sn <- sampleNames(eset)
# eSet 2 is constructed
es2 <- new("eSet", phenoData=pd, assayData=xl,
reporterNames=gn, sampleNames=sn)
# illustrate subset and show for assayData as list
es2[1:4,1:4]
# build with environment assayData
eenv <- new.env()
assign("e1", assayData(eset), eenv)
es3 <- new("eSet", phenoData=pd, assayData=eenv,
reporterNames=gn, sampleNames=sn)
es3
es3[1:5,1:5]
# show some legacy behavior: set list element name to
# exprs and invoke exprs()
names(assayData(es2)) <- "exprs"
dim(exprs(es2))
# show some validity checking
assayData(es3) <- assayData(es2)
es3 # now has list
sampleNames(es2) <- letters # ok
if (interactive()) {
lk <- try(sampleNames(es2) <- letters[-1]) # not ok
lk
lk <- try(assayData(es2) <- assayData(es2[-1,])) # not ok
class(lk)
}
# work with the swirl data
data(SW)
data(swrep)
data(SWPD)
sw <- new("eSet",
assayData=list( R=SW$R, G=SW$G, Rb=SW$Rb, Gb=SW$Gb),
phenoData=SWPD, reporterInfo=swrep, sampleNames=as.character(1:4),
reporterNames=as.character(swrep$Name))