ACMESet-class {ACME} | R Documentation

## Class "ACMESet"

### Description

An extension of ExpressionSet to deal with ACME data including chromosome locations

### Objects from the Class

Objects can be created by calls of the form `new("ACMESet", assayData, phenoData, featureData, experimentData, annotation, exprs, ...)`. The exprs assayDataElement stores the data. The featureData slot stores the chromosome location. In practice, the data.frame underlying the featureData MUST contain three columns named chromosome, start, and end; this is enforced by the class validity method.

### Slots

`assayData`:

  Object of class `"AssayData"`. See ExpressionSet for details.

`phenoData`:

  Object of class `"AnnotatedDataFrame"` See ExpressionSet for details.

`featureData`:

  Object of class `"AnnotatedDataFrame"` See ExpressionSet for details.

`experimentData`:

  Object of class `"MIAME"` See ExpressionSet for details.

`annotation`:

  Object of class `"character"` See ExpressionSet for details.

`.__classVersion__`:

  Object of class `"Versions"` See ExpressionSet for details.

### Extends

Class `"ExpressionSet"`, directly. Class `"eSet"`, by class "ExpressionSet", distance 2. Class `"VersionedBiobase"`, by class "ExpressionSet", distance 3. Class `"Versioned"`, by class "ExpressionSet", distance 4.

### Methods

chromosome

  `signature(object = "ACMESet")`: Accessor for the chromosome. Returns a vector of chromosomes.

end

  `signature(x = "ACMESet")`: Accessor for the end location for a probe. If that is not known, this could be set to the same value as the start location.

plot

  `signature(x = "ACMESet")`: A convenience plotting method that takes a sample name and chrom as well.

start

  `signature(x = "ACMESet")`: Accessor for the start location for a probe.

### Author(s)

Sean Davis <sdavis2@mail.nih.gov>

### See Also

`ExpressionSet`, `ACMECalcSet`

### Examples

    showClass("ACMESet")
    data(example.agff)
    example.agff
    head(chromosome(example.agff))
    head(start(example.agff))
    head(end(example.agff))

[Package ACME version 2.36.0 Index]