GreyListChIP (version 1.4.0)

loadKaryotype-methods: Load a karyotype from a file

Description

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

Usage

loadKaryotype(obj, karyoFile, tileSize=1024)

Arguments

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.

Value

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

See Also

GreyList

Examples

# 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(gl,fn)