cpgdensity: Get CpG density for genomic regions
In charm: Analysis of DNA methylation data from CHARM microarrays

Description Usage Arguments Details Value Author(s) Examples

Calculate the CpG density for a set of windows

1	cpgdensity(subject, chr, pos, windowSize = 500, sequence = "CG")

`subject`	BSGenome object (e.g. Hsapiens)
`chr`	character vector
`pos`	numeric vector
`windowSize`	number value
`sequence`	character string

Calculate the CpG density for a set of regions. chr and pos specify the region mid-points and windowSize specifies the size of the window to be centered on these mid-points. i.e. The window will stretch from pos-windowSize/2 to pos+windowSize/2.

a numeric vector

Martin Aryee <aryee@jhu.edu>

	if (require(BSgenome.Hsapiens.UCSC.hg18)){
		chr <- c("chr1", "chr1", "chr2")
		pos <- c(100000, 100500, 100000)
		cpgd <- cpgdensity(Hsapiens, chr=chr, pos=pos, windowSize = 500)
		cpgd
	}