edmr: Empirical differentially methylated regions

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

Description

Comprehensive DMR analysis based on bimodal normal distribution model and weighted cost function for regional methylation analysis optimization. It captures the regional methylation modification by taking the spatial distribution of CpGs into account for the enrichment DNA methylation sequencing data so as to optimize the definition of the empirical regions. Combined with the dependent adjustment for regional p-value combination.

Usage

edmr(myDiff, step = 100, dist = "none", DMC.qvalue = 0.01,
  DMC.methdiff = 25, num.DMCs = 1, num.CpGs = 3, DMR.methdiff = 20,
  plot = FALSE, main = "", mode = 1, ACF = TRUE, fuzzypval = 1)

Arguments

myDiff	a myDiff object from methylKit package. Required.
step	a numeric variable for calculating auto-correlation, default: 100.
dist	distance cutoff to call a gap for DMR, default: "none", which will be automatically determined by the bimodal normal distribution, default: 100.
DMC.qvalue	qvalue cutoff for DMC definition, default: 0.01
DMC.methdiff	methylation difference cutoff for DMC definition, default: 25.
num.DMCs	cutoff of the number DMCs in each region to call DMR, default: 1.
num.CpGs	cutoff of the number of CpGs, default: 3.
DMR.methdiff	cutoff of the DMR mean methylation difference, default=20.
plot	plot the bimodal normal distribution fitting or not, default=FAlSE.
main	the title of the plot, if plot=TRUE. Default=FALSE.
mode	the mode of call DMRs. 1: using all CpGs together. 2: use unidirectional CpGs to call DMRs. default: 1.
ACF	p-value combination test with (TRUE, default) or without (FALSE) dependency adjustment.
fuzzypval	p-value cutoff for raw regions definition.

Value

GRanges

Examples

library(methylKit)
library(GenomicRanges)
library(mixtools)
library(data.table)
data(edmr)
mydmr=edmr(chr22.myDiff, mode=1, ACF=TRUE)
mysigdmr=filter.dmr(mydmr)
mydmr2=edmr(chr22.myDiff, mode=2, ACF=TRUE)
mydmr3=edmr(chr22.myDiff, mode=1, ACF=FALSE)
mydmr4=edmr(chr22.myDiff, mode=2, ACF=FALSE)

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