FeatureSet-class {oligoClasses} | R Documentation

## "FeatureSet" and "FeatureSet" Extensions

### Description

Classes to store data from Expression/Exon/SNP/Tiling arrays at the feature level.

### Objects from the Class

The FeatureSet class is VIRTUAL. Therefore users are not able to create instances of such class.

Objects for FeatureSet-like classes can be created by calls of the form: `new(CLASSNAME, assayData, manufacturer, platform, exprs, phenoData, featureData, experimentData, annotation, ...)`. But the preferred way is using parsers like `read.celfiles` and `read.xysfiles`.

### Slots

`manufacturer`:

  Object of class `"character"`

`assayData`:

  Object of class `"AssayData"`

`phenoData`:

  Object of class `"AnnotatedDataFrame"`

`featureData`:

  Object of class `"AnnotatedDataFrame"`

`experimentData`:

  Object of class `"MIAME"`

`annotation`:

  Object of class `"character"`

`.__classVersion__`:

  Object of class `"Versions"`

### Methods

show

  `signature(.Object = "FeatureSet")`: show object contents

bothStrands

  `signature(.Object = "SnpFeatureSet")`: checks if object contains data for both strands simultaneously (50K/250K Affymetrix SNP chips - in this case it returns TRUE); if object contains data for one strand at a time (SNP 5.0 and SNP 6.0 - in this case it returns FALSE)

### Author(s)

Benilton Carvalho

### See Also

`eSet`, `VersionedBiobase`, `Versioned`

### Examples

    set.seed(1)
    tmp <- 2^matrix(rnorm(100), ncol=4)
    rownames(tmp) <- 1:25
    colnames(tmp) <- paste("sample", 1:4, sep="")
    efs <- new("ExpressionFeatureSet", exprs=tmp)

[Package oligoClasses version 1.42.0 Index]