MultiSet {Biobase} | R Documentation

## Class to Contain and Describe High-Throughput Expression Level Assays.

### Description

Container for high-throughput assays and experimental metadata. `MutliSet` is derived from `eSet-class`. `MultiSet` differs from `ExpressionSet-class` because `MultiSet` can contain any element(s) in `assayData` (`ExpressionSet` must have an element named `exprs`).

### Extends

Directly extends class `eSet`.

### Creating Objects

`new('MultiSet', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], ...)`

`updateOldESet(oldESet,"MultiSet")`

`MultiSet` instances are usually created through `new("MultiSet", ...)`. The `...` arguments to `new` are matrices of expression data (with features corresponding to rows and samples to columns), `phenoData`, `experimentData`, and `annotation`. `phenoData`, `experimentData`, and `annotation` can be missing, in which case they are assigned default values.

`updateOldESet` will take a serialized instance (e.g., saved to a disk file with `save` object created with earlier definitions of the `eSet-class`, and update the object to `MultiSet`. Warnings are issued when direct translation is not possible; incorrectly created `oldESet` instances may not be updated.

### Slots

Inherited from `eSet`:

`assayData`:
  Contains zero or more matrices with equal dimensions, and with column number equal to `nrow(phenoData)`. Each matrix in `assayData` has rows represening features (e.g., reporters) and columns representing samples. Class:`AssayData-class`
`phenoData`:
  See `eSet-class`
`experimentData`:
  See `eSet-class`
`annotation`:
  See `eSet-class`

### Methods

Class-specific methods: none

Derived from `eSet-class`:

`sampleNames(MultiSet)` and `sampleNames(MultiSet)<-`:
  See `eSet-class`
`featureNames(MultiSet)`, `featureNames(MultiSet, value)<-`:
  See `eSet-class`
`dims(MultiSet)`:
  See `eSet-class`
`phenoData(MultiSet)`, `phenoData(MultiSet,value)<-`:
  See `eSet-class`
`varLabels(MultiSet)`, `varLabels(MultiSet, value)<-`:
  See `eSet-class`
`varMetadata(MultiSet)`, `varMetadata(MultiSet,value)<-`:
  See `eSet-class`
`pData(MultiSet)`, `pData(MultiSet,value)<-`:
  See `eSet-class`
`varMetadata(MultiSet)`, `varMetadata(MultiSet,value)`
  See `eSet-class`
`experimentData(MultiSet)`,`experimentData(MultiSet,value)<-`:
  See `eSet-class`
`pubMedIds(MultiSet)`, `pubMedIds(MultiSet,value)`
  See `eSet-class`
`abstract(MultiSet)`:
  See `eSet-class`
`annotation(MultiSet)`, `annotation(MultiSet,value)<-`
  See `eSet-class`
`combine(MultiSet,MultiSet)`:
  See `eSet-class`
`storageMode(eSet)`, `storageMode(eSet,character)<-`:
  See `eSet-class`
`reporterNames(MultiSet)`, `reporterNames(MultiSet,value)<-`:
  DEPRECATED

Standard generic methods:

`initialize(MultiSet)`:
  Object instantiation, used by `new`; not to be called directly by the user.
`validObject(MultiSet)`:
  Validity-checking method, ensuring that all elements of `assayData` are matricies with equal dimensions.
`show(MultiSet)`
  See `eSet-class`
`dim(MultiSet)`, `ncol`
  See `eSet-class`
`MultiSet[(index)`:
  See `eSet-class`
`MultiSet$`, `MultiSet$<-`
  See `eSet-class`

### Author(s)

Biocore team

### See Also

`eSet-class`, `ExpressionSet-class`

### Examples

    # create an instance of ExpressionSet
    new("ExpressionSet")

    # update existing exprSet-like class to ExpressionSet
    data(sample.exprSet)
    expressionSet <- as(sample.exprSet,"ExpressionSet")
    expressionSet

    # information about assay and sample data
    featureNames(expressionSet)[1:10]
    sampleNames(expressionSet)[1:5]
    phenoData(expressionSet)
    experimentData(expressionSet)

    # subset: first 10 genes, samples 2, 4, and 10
    expressionSet <- as(sample.exprSet,"ExpressionSet")
    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]

[Package Biobase version 1.10.1 Index]