# 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`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

1 2 3 | ```
data(example.agff)
example.agffcalc <- do.aGFF.calc(example.agff,window=1000,thresh=0.9)
example.agffcalc
``` |