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

In benilton/oligoClassesOld: 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

	if(require("VanillaICE")){
		library(oligoClasses)
		library(GenomicRanges)
		library(Biobase)
		library(foreach)
		registerDoSEQ()
		data(oligoSetExample, package="oligoClasses")
		oligoSet <- oligoSet[chromosome(oligoSet) == 1, ]
		grl <- hmm(oligoSet,TAUP=1e10)
		class(grl)## GRangesList
		gr <- grl[[1]]
		(frange <- makeFeatureGRanges(oligoSet))
		## which features overlap with the second range in sample NA06993
		subsetByOverlaps(frange, gr[2,])
	}

benilton/oligoClassesOld documentation built on May 12, 2019, 11:51 a.m.