oligoClasses (version 1.34.0)

GenomeAnnotatedDataFrameFrom-methods: Methods for Function GenomeAnnotatedDataFrameFrom in Package oligoClasses

Description

GenomeAnnotatedDataFrameFrom is a convenience for creating GenomeAnnotatedDataFrame objects.

Methods

Use the method with GenomeAnnotatedDataFrameFrom(object, annotationPkg, genome, ...); the argument annotationPkg must be specified for matrix and AssayData classes.

signature(object="assayData")

This method creates an GenomeAnnotatedDataFrame using feature names and dimensions of an AssayData object as a template.

signature(object="matrix")

This method creates an GenomeAnnotatedDataFrame using row names and dimensions of a matrix object as a template.

signature(object="NULL")

This method (called with 'NULL' as the object) creates an empty GenomeAnnotatedDataFrame.

signature(object="array")

This method (called with 'array' as the object) creates a GenomeAnnotatedDataFrame using the first dimension of the array (rows are the number of features).

Examples

	require(Biobase)
	minReqVersion <- "1.0.2"
	require(human370v1cCrlmm)
	if (packageDescription("human370v1cCrlmm", fields='Version') >= minReqVersion){
		x <- matrix(1:25, 5, 5,
			    dimnames=list(c("rs10000092","rs1000055", "rs100016", "rs10003241", "rs10004197"), NULL))
		gd <- GenomeAnnotatedDataFrameFrom(x, annotationPkg="human370v1cCrlmm",
						   genome="hg18")
		pData(gd)
		chromosome(gd)
		position(gd)
	}