gSetList-class {oligoClasses} | R Documentation

## Virtual Class for Lists of eSets

### Description

Virtual Class for Lists of eSets.

### Objects from the Class

A virtual Class: No objects may be created from it.

### Slots

`assayDataList`:

  Object of class `"AssayData"` ~~

`phenoData`:

  Object of class `"AnnotatedDataFrame"` ~~

`protocolData`:

  Object of class `"AnnotatedDataFrame"` ~~

`experimentData`:

  Object of class `"MIAME"` ~~

`featureDataList`:

  Object of class `"list"` ~~

`chromosome`:

  Object of class `"vector"` ~~

`annotation`:

  Object of class `"character"` ~~

`genome`:

  Object of class `"character"` ~~

### Accessors

`object` is an instance of a `gSetList`-derived class.

  `annotation(object)`:

  character string indicating the package used to provide annotation for the features on the array.

  `chromosome(object)`:

  Returns the chromosome corresponding to each element in the `gSetList` object

  `elementNROWS(object)`: Returns the number of rows for each list of assays. In most `gSetList`-derived classes, the assays are organized by chromosome and `elementNROWS` returns the number of markers for each chromosome.

  `genomeBuild(object)`, `genomeBuild(object) <- value`:

  Get or set the UCSC genome build. Supported builds are hg18 and hg19.

### Coercion

`object` is an instance of a `gSetList`-derived class.

  `makeFeatureGRanges(object, ...)`:

  Create a GRanges object for the featureData. The featureData is stored as a list. This method stacks the featureData from each list element. Metadata columns in the GRanges object include physical position ('position'), a SNP indicator ('isSnp'), and the chromosome. The genome build is extracted from `object` using the method `genomeBuild`.

### Author(s)

R. Scharpf

### See Also

`oligoSetList`, `BeadStudioSetList`

### Examples

    showClass("gSetList")

[Package oligoClasses version 1.50.4 Index]