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 1.9.2 Index]