copynumber: Retrieve copynumber data from cgh objects.

In tgac-vumc/CGHbase: CGHbase: Base functions and classes for arrayCGH data analysis.

Description

These generic functions access the copynumber values of assay data stored in an object derived from the cghRaw-class, cghSeg-class or cghCall-class.

Usage

copynumber(object)
copynumber(object) <- value
segmented(object)
segmented(object) <- value
calls(object)
calls(object) <- value

Arguments

object	Object derived from class cghRaw, cghSeg, or cghCall
value	Matrix with rows representing features and columns samples.

Value

copynumber returns a matrix of copynumber values;

Author(s)

Sjoerd Vosse

See Also

cghRaw-class, cghSeg-class, cghCall-class

Examples

	data(WiltingCalled)
	log2ratios <- copynumber(WiltingCalled)
	segments <- segmented(WiltingCalled)
	calls <- calls(WiltingCalled)	

tgac-vumc/CGHbase documentation built on May 31, 2019, 8:59 a.m.