filter.dmr: significant DMRs

In Shicheng-Guo/edmr: Empirical differentially methylated regions calculation

Description

significant DMRs

Usage

filter.dmr(myDMR, DMR.qvalue = 0.001, mean.meth.diff = 20, num.CpGs = 5,
  num.DMCs = 3)

Arguments

myDMR	a GRanges object for DMR regions called.
DMR.qvalue	qvalue cutoff for DMC definition, default: 0.001
mean.meth.diff	cutoff of the DMR mean methylation difference, default=20
num.CpGs	cutoff of the number DMCs in each region to call DMR, default: 5
num.DMCs	cutoff of the number of CpGs, default: 3

Examples

library(methylKit)
library(GenomicRanges)
library(mixtools)
library(data.table)
data(edmr)
mydmr=edmr(chr22.myDiff, mode=1, ACF=TRUE)
mysigdmr=filter.dmr(mydmr)

Shicheng-Guo/edmr documentation built on May 9, 2019, 1:27 p.m.