charm (version 2.18.0)

cpgdensity: Get CpG density for genomic regions

Description

Calculate the CpG density for a set of windows

Usage

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

Arguments

subject

BSGenome object (e.g. Hsapiens)

chr

character vector

pos

numeric vector

windowSize

number value

sequence

character string

Value

a numeric vector

Details

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.

Examples

	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
	}