aGFFCalc-class {ACME} | R Documentation

## Class "aGFFCalc"

### Description

Store results of ACME calculations

### Objects from the Class

Objects can be created by calls of the form `new("aGFFCalc", ...)`.

### Slots

`call`:

  Object of class `"call"`, contains the exact call to do.aGFF.calc, for historical purposes

`threshold`:

  Object of class `"numeric"`, the threshold used in the calculation

`cutpoints`:

  Object of class `"numeric"`, the data value above which probes were considered positive

`vals`:

  Object of class `"matrix"`, equivalent in size to the original data matrix, containing the calculated p-values from the ACME algorithm

`annotation`:

  Object of class `"data.frame"`, currently a copy of the original annotation, possibly reordered in chromosome order

`data`:

  Object of class `"matrix"`, the original data, possibly reordered

`samples`:

  Object of class `"data.frame"`, sample metadata

### Extends

Class `"aGFF"`, directly.

### Methods

plot

  `signature(x = "aGFFCalc", ask=FALSE)`: plot the results of an ACME calculation

print

  `signature(x = "aGFFCalc")`: brief overview of the object

show

  `signature(object = "aGFFCalc")`: brief overview of the object

### Author(s)

Sean Davis <sdavis2@mail.nih.gov>

### See Also

`do.aGFF.calc`, `aGFF-class`

### Examples

    data(example.agff)
    example.agffcalc <- do.aGFF.calc(example.agff,window=1000,thresh=0.9)
    example.agffcalc

[Package ACME version 2.40.0 Index]