makeFeatureGRanges: Construct a GRanges object from several possible...

In jmacdon/oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

Description

Construct a GRanges object from several possible feature-level classes. The conversion is useful for subsequent ranged-data queries, such as findOverlaps, countOverlaps, etc.

Usage

makeFeatureGRanges(object, ...)

Arguments

object	A gSet-derived object containing chromosome and physical position for the markers on the array.
...	See the makeFeatureGRanges method for GenomeAnnotatedDataFrame.

Value

A GRanges object.

Author(s)

R. Scharpf

See Also

findOverlaps, GRanges, GenomeAnnotatedDataFrame

Examples

  library(oligoClasses)
	library(GenomicRanges)
	library(Biobase)
	library(foreach)
	registerDoSEQ()
	data(oligoSetExample, package="oligoClasses")
	oligoSet <- oligoSet[chromosome(oligoSet) == 1, ]
  makeFeatureGRanges(oligoSet)

jmacdon/oligoClasses documentation built on Aug. 11, 2020, 12:32 a.m.