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 2.48.0 Index]