ACMECalcSet-class {ACME}R Documentation

Class "ACMECalcSet"

Description

A subclass of ACMESet that can also store the parameters and results of an ACME calculation

Objects from the Class

Objects can be created by calls of the form new("ACMECalcSet", assayData, phenoData, featureData, experimentData, annotation, cutpoints, threshold, exprs, vals, ...). In addition to the constraints defined by ACMESet, this class can also hold the results (in the assayDataElement vals) and the threshold and cutpoints from an ACME do.aGFF.calc run

Slots

cutpoints:

Object of class "numeric" The values of the cutpoints used in an analysis by do.aGFF.calc, one per sample.

threshold:

Object of class "numeric" The threshold used in an analysis.

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 "ACMESet", directly. Class "ExpressionSet", by class "ACMESet", distance 2. Class "eSet", by class "ACMESet", distance 3. Class "VersionedBiobase", by class "ACMESet", distance 4. Class "Versioned", by class "ACMESet", distance 5.

Methods

cutpoints

signature(x = "ACMECalcSet"): A simple getter for the cutpoints.

plot

signature(x = "ACMECalcSet"): A convenience plotting method that also takes sample and chrom

show

signature(object = "ACMECalcSet"): A show method

threshold

signature(x = "ACMECalcSet"): A simple getter for the threshold

vals

signature(x = "ACMECalcSet"): an accessor for the p-values from a run of do.aGFF.calc. Returns a matrix with samples in columns and probes in rows.

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

See Also

ACMESet

Examples

showClass("ACMECalcSet")
data(example.agff)
b <- do.aGFF.calc(example.agff,thresh=0.95,window=1000)
b
head(vals(b))
threshold(b)
cutpoints(b)

[Package ACME version 2.36.0 Index]