GreyListChIP (version 1.4.0)

greyListBS: Construct a grey list with default arguments

Description

This function is a convenience function, wrapping several steps of grey list construction into one step. If you are content to accept the package's defaults, and are using a BSgenome object to supply the karyotype, this function might be of use to you.

Usage

greyListBS(genome, bam)

Arguments

genome

a BSgenome object, for the relevant genome.

bam

a BAM file to use for making the grey list.

Value

An object of class GreyList.

See Also

GreyList

Examples

# If you want to accept the defaults for everything, you can create the
# GreyList in one step using a BSgenome object:
library(BSgenome.Hsapiens.UCSC.hg19)
path <- system.file("extra", package="GreyListChIP")
## Not run: fn <- file.path(path,"sample_chr21.bam")
## Not run: gl <- greyListBS(BSgenome.Hsapiens.UCSC.hg19,fn)