rCGH-class {rCGH} | R Documentation

## Class `"rCGH"`

### Description

Class `"rCGH"` is a superclass living on top of `"rCGH-Agilent"`, `"rCGH-SNP6"`, `"rCGH-cytoScan"`, `"rCGH-oncoScan"`, and `"rCGH-generic"`. These objects inherit most of the properties of the superclass, and allow specific parameterizations used during the analysis process.
Objects are created by platform-specific `read` functions: `"readAgilent"`, `"readAffySNP6"`, and `"readAffyCytoScan"`, each corresponding to their matched file format.
A supplementary `"readGeneric"` allows the user to create a `"rCGH"` object from custom arrays. Slots described below are used to store sample information and analysis parameters, as well as segmentation results. All are accessible through specific `"Accessors"` functions.

### Objects from the Class

Objects can be created by calls of the form `new("rCGH", ...)`.
Slots content are updated at each different analysis step, and are accessible through specific `get` functions.

### Slots

`info`:

  Object of class `"character"`: where sample information can be stored. See `"getInfo"` and `"setInfo"`.

`cnSet`:

  Object of class `"data.frame"`: the full data set. See `"getCNset"`.

`param`:

  Object of class `"list"`: the analysis parameters stored for traceability. See `"getParam"`.

`segTable`:

  Object of class `"data.frame"`: the segmentation table. See `"getSegTable"`.

### Methods

show

  `signature(object = "rCGH")`: ...

### Author(s)

Frederic Commo

### See Also

`"rCGH-Agilent"`, `"rCGH-SNP6"`, `"rCGH-cytoScan"`, `"rCGH-generic"`

### Examples

    showClass("rCGH")

[Package rCGH version 1.20.0 Index]