ACMESet-class: Class "ACMESet"

In ACME: Algorithms for Calculating Microarray Enrichment (ACME)

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 <[e-mail]>

See Also

ExpressionSet, ACMECalcSet

Examples

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

ACME documentation built on Nov. 8, 2020, 7:51 p.m.