NChannelSet-class {Biobase} | R Documentation

## Class to contain data from multiple channel array technologies

### Description

Container for high-throughput assays and experimental meta-data. Data are from experiments where a single ‘chip’ contains several (more than 1) different ‘channels’. All channels on a chip have the same set of‘features’. An experiment consists of a collection of several N-channel chips; each chip is a ‘sample’.

An `NChannelSet` provides a way to coordinate assay data (expression values) with phenotype information and references to chip annotation data; it extends the `eSet` class.

An `NChannelSet` allows channels to be extracted (using the `channels` method, mentioned below), and subsets of features or samples to be selected (using `[<features>, <samples>]`). Selection and subsetting occur so that relevant phenotypic data is maintained by the selection or subset.

### Objects from the Class

Objects can be created by calls of the form `NChannelSet( assayData, phenoData, ...)`. See the examples below.

### Slots

`assayData`:

  Object of class `AssayData`, usually an environment containing matrices of identical size. Each matrix represents a single channel. Columns in each matrix correspond to samples, rows to features. Once created, `NChannelSet` manages coordination of samples and channels.

`phenoData`:

  Object of class `AnnotatedDataFrame`.

  The `data` component of the `AnnotatedDataFrame` is `data.frame` with number of rows equal to the number of samples. Columns of the `data` component correspond to measured covariates.

  The `varMetadata` component consists of mandatory columns `labelDescription` (providing a textual description of each column label in the `data` component) and `channel`. The `channel` of `varMetadata` is a `factor`, with levels equal to the names of the `assayData` channels, plus the special symbol `_ALL_`. The `channel` column is used to indicate which channel(s) the corresponding column in the `data` component of `AnnotatedDataFrame` correspond; the `_ALL_` symbol indicates that the `data` column is applicable to all channels. `varMetadata` may contain additional columns with arbitrary information.

  Once created, `NChannelSet` coordinates selection and subsetting of channels in `phenoData`.

`featureData`:

  Object of class `AnnotatedDataFrame`, used to contain feature data that is unique to this experiment; feature-level descriptions common to a particular chip are usually referenced through the `annotation` slot.

`experimentData`:

  Object of class `MIAME` containing descriptions of the experiment.

`annotation`:

  Object of class `"character"`. Usually a length-1 character string identifying the chip technology used during the experiment. The annotation string is used to retrieve information about features, e.g., using the `annotation` package.

`protocolData`:

  Object of class `"character"`. A character vector identifying the dates the samples were scanned during the experiment.

`.__classVersion__`:

  Object of class `Versions`, containing automatically created information about the class definition Biobase package version, and other information about the user system at the time the instance was created. See `classVersion` and `updateObject` for examples of use.

### Extends

Class `"eSet"`, directly. Class `"VersionedBiobase"`, by class "eSet", distance 2. Class `"Versioned"`, by class "eSet", distance 3.

### Methods

Methods with class-specific functionality:

`channel(object, name, ...)`

  `signature(object="NChannelSet", name="character")`. Return an `ExperessionSet` created from the channel and corresponding phenotype of argument `name`. `name` must have length 1. Arguments `...` are rarely used, but are passed to the `ExpressionSet` constructor, for instance to influence `storage.mode`.

`channelNames(object)`, `channelNames(object) <- value`

  `signature(object = "NChannelSet")`. Obtain, reorder, or rename channels contained in `object`. See `channelNames`.

`selectChannels(object, names, ...`

  `signature(object = "NChannelSet", names = "character")`. Create a new `NChannelSet` from `object`, containing only channels in `names`. The `...` is not used by this method.

`object[features, samples]`

  `signature(object = "NChannelSet", features = "ANY", samples = "ANY")`. Create a new `NChannelSet` from `object`, containing only elements matching `features` and `samples`; either index may be missing, or a character, numeric, or logical vector.

`sampleNames(object) <- value`

  `signature(object = "NChannelSet", value = "list")` assign each (named) element of `value` to the `sampleNames` of the correspondingly named elements of `assayData` in `object`.

Methods with functionality derived from `eSet`: `annotation`, `annotation<-`, `assayData`, `assayData<-`, `classVersion`, `classVersion<-`, `dim`, `dims`, `experimentData`, `experimentData<-`, `featureData`, `featureData<-`, `phenoData`, `phenoData<-`, `protocolData`, `protocolData<-`, `pubMedIds`, `pubMedIds<-`, `sampleNames`, `sampleNames<-`, `storageMode`, `storageMode<-`, `varMetadata`, `varMetadata<-`, `isCurrent`, `isVersioned`, `updateObject`.

Additional methods: `coerce` (‘as’, to convert between objects, if possible), `initialize` (used internally for creating objects), `show` (invoked automatically when the object is displayed to the screen)

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### See Also

`eSet`, `ExpressionSet`.

### Examples

    ## An empty NChannelSet
    obj <- NChannelSet()

    ## An NChannelSet with two channels (R, G) and no phenotypic data
    obj <- NChannelSet(R=matrix(0,10,5), G=matrix(0,10,5))

    ## An NChannelSet with two channels and channel-specific phenoData
    R <- matrix(0, 10, 3, dimnames=list(NULL, LETTERS[1:3]))
    G <- matrix(1, 10, 3, dimnames=list(NULL, LETTERS[1:3]))
    assayData <- assayDataNew(R=R, G=G)
    data <- data.frame(ChannelRData=numeric(ncol(R)),
                       ChannelGData=numeric(ncol(R)),
                       ChannelRAndG=numeric(ncol(R)))
    varMetadata <- data.frame(labelDescription=c(
                                "R-specific phenoData",
                                "G-specific phenoData",
                                "Both channel phenoData"),
                              channel=factor(c("R", "G", "_ALL_")))
    phenoData <- AnnotatedDataFrame(data=data, varMetadata=varMetadata)
    obj <- NChannelSet(assayData=assayData, phenoData=phenoData)
    obj

    ## G channel as NChannelSet
    selectChannels(obj, "G")

    ## G channel as ExpressionSet
    channel(obj, "G")

    ## Samples "A" and "C"
    obj[,c("A", "C")]

[Package Biobase version 2.40.0 Index]