setRegions-methods: Replace the set of regions of a 'GreyList' object
In GreyListChIP: Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Description Usage Arguments Value Author(s) See Also Examples

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.

1	setRegions(obj, regions, tileSize=1024)

`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.

Returns the GreyList object with a new tiling.

Gord Brown

GreyList, GRanges

# 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)