cpgdensity {charm} | R Documentation |
Calculate the CpG density for a set of windows
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 }