rCGH-class: Class '"rCGH"'

In rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

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")

rCGH documentation built on Nov. 8, 2020, 8:30 p.m.