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], protocolData = [AnnotatedDataFrame], ...)`

`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`, `annotation`, and `protocolData`. `phenoData`, `experimentData`, `annotation`, and `protocolData` 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 representing features (e.g., reporters) and columns representing samples. Class:`AssayData-class`

`phenoData`:

  See `eSet-class`

`experimentData`:

  See `eSet-class`

`annotation`:

  See `eSet-class`

`protocolData`:

  See `eSet-class`

### Methods

Class-specific methods: none

Derived from `eSet-class`:

`updateObject(object, ..., verbose=FALSE)`

  Update instance to current version, if necessary. See `updateObject` and `eSet`

`isCurrent(object)`

  Determine whether version of object is current. See `isCurrent`

`isVersioned(object)`

  Determine whether object contains a 'version' string describing its structure . See `isVersioned`

`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`

`protocolData(MultiSet)`, `protocolData(MultiSet,value)<-`

  See `eSet-class`

`combine(MultiSet,MultiSet)`:

  See `eSet-class`

`storageMode(eSet)`, `storageMode(eSet,character)<-`:

  See `eSet-class`

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.

`as(eSet,MultiSet)`:

  Coerce the `eSet` portion of an object to `MultiSet`.

`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("MultiSet")

[Package Biobase version 2.40.0 Index]