setRegions-methods {GreyListChIP}R Documentation

Replace the set of regions of a GreyList object

Description

Though a BSgenome object (or a karyotype file, or a GRanges) is supplied when the GreyList object is created, it is conceivable that the user might want to replace it. This method allows that.

Usage

setRegions(obj, regions, tileSize=1024)

Arguments

obj

A GreyList object.

regions

A GRanges object, from which to take the karyotype.

tileSize

The size in nucleotides of each tile. Overlapping tiles will be generated, spaced at 1/2 the width of the tiles.

Value

Returns the GreyList object with a new tiling.

Author(s)

Gord Brown

See Also

GreyList, GRanges

Examples

# Load a pre-built GreyList objct.
data(greyList)

# Replace the karyotype, updating the genome tiling.
regions=GRanges(seqnames=Rle(c('chr21','chr21','chr22')),
                ranges=IRanges(c(1,20000,30000),end=c(10000,30000,40000)))
gl <- setRegions(greyList,regions)

[Package GreyListChIP version 1.26.0 Index]