GreyListChIP (version 1.4.0)

getKaryotype-methods: Replace the karyotype of a GreyList object

Description

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

Usage

getKaryotype(obj, genome, tileSize=1024)

Arguments

obj

A GreyList object.

genome

A BSgenome 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 genome and tiling.

See Also

GreyList, BSgenome

Examples

# Load a pre-built GreyList objct.
data(greyList)
library(BSgenome.Hsapiens.UCSC.hg19)

# Replace the karyotype, updating the genome tiling.
## Not run: gl <- getKaryotype(gl,BSgenome.Hsapiens.UCSC.hg19)