MEDME (version 1.32.0)

CGcount: Determining the count of CpG dinucleotides for a set of genomic locations

Description

The count of CpGs is determined in each window of size wsize, with or withouth weighting, for each probe according to its position, chromosome and genome realease

Usage

CGcount(data, wsize = 1000, wFunction = "linear")

Arguments

data

An object of class MEDMEset

wsize

number; the size of the smoothing window, in bp

wFunction

string; the type of weighting function, to choose among linear, exp, log or none

Value

An object of class MEDMEset is returned where the count of CpGs for each probe has been saved on the CGcount slot.

Details

Only human and mouse are currently supported. The respective genomic sequence metadata library needs to be downloaded from the Bioconductor website, installed and loaded (around 800Mb). Please note that only the last genome release should be used. LiftOver UCSC tool could be used for batch conversion of old genomic position to the last genome release.

See Also

smooth

Examples

data(testMEDMEset)
## just an example with the first 1000 probes
testMEDMEset = smooth(data = testMEDMEset[1:1000,])
library(BSgenome.Hsapiens.UCSC.hg18)
testMEDMEset = CGcount(data = testMEDMEset)