ACMESet-class {ACME} | R Documentation |
An extension of ExpressionSet to deal with ACME data including chromosome locations
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.
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.
Class "ExpressionSet"
, directly.
Class "eSet"
, by class "ExpressionSet", distance 2.
Class "VersionedBiobase"
, by class "ExpressionSet", distance 3.
Class "Versioned"
, by class "ExpressionSet", distance 4.
signature(object = "ACMESet")
: Accessor for
the chromosome. Returns a vector of chromosomes.
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.
signature(x = "ACMESet")
: A convenience plotting
method that takes a sample name and chrom as well.
signature(x = "ACMESet")
: Accessor for the start
location for a probe.
Sean Davis <sdavis2@mail.nih.gov>
showClass("ACMESet") data(example.agff) example.agff head(chromosome(example.agff)) head(start(example.agff)) head(end(example.agff))