loadKaryotype-methods: Load a karyotype from a file
In GreyListChIP: Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Description Usage Arguments Value Author(s) See Also Examples

Load a karyotype from a file, (re)generate the tiling, for a GreyList object.

1	loadKaryotype(obj, karyoFile, tileSize=1024)

`obj`	A `GreyList` object to set a new karyotype for.
`karyoFile`	A text file describing a genome's karyotype. The format is one line per chromosome (or contig or whatever), with the name of the chromosome, some white space, and an integer giving the length of the chromosome in nucleotides.
`tileSize`	The width of tiles on which to count. Tiles will be placed every tileSize/2 nucleotides, to catch regions of high signal that might otherwise be split across (non-overlapping) tiles and hence missed.

Returns the GreyList object with a new genome and tiling, loaded from the provided file.

Gord Brown

GreyList

# load a pre-built GreyList object:
data(greyList)

# Get a karyotype file:
path <- system.file("extra", package="GreyListChIP")
fn <- file.path(path,"karyotype_chr21.txt")

# Replace the karyotype in the GreyList:
gl <- loadKaryotype(greyList,fn)