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 1.2.1 Index]