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
:
reporterInfo
data.frameOrNULL
phenoData
phenoData
Introduced in eSet
:
assayData
:phenoData
pData
slot; class:listOrEnv
sampleNames
:character
reporterNames
:character
description
:class:characterORMIAME
notes
:character
annotation
:character
history
:character
Derived from annotatedDataset
:
$(eSet)
and $(eSet, value)<-
annotatedDataset
phenoData(eSet)
and phenoData(eSet, value)<-
annotatedDataset
reporterInfo(eSet)
and reporterInfo(eSet, value)<-
annotatedDataset
pData(eSet)
and pData(eSet, value)<-
annotatedDataset
[[(index)
and [[(index, value)<-
:annotatedDataset
varLabels(eSet)
annotatedDataset
Class-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))