filter.dmr: significant DMRs

Description Usage Arguments Examples

View source: R/filter.dmr.R

Description

significant DMRs

Usage

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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

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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 10, 2017, 1:36 p.m.