install.packages( c("data.table", "mixtools", "devtools"))
source("http://bioconductor.org/biocLite.R")
biocLite(c("GenomicRanges","IRanges"))
# install from github
library(devtools)
install_github("edmr", username = "ShengLi",build_vignettes=FALSE)

library(edmr)
library(GenomicRanges)
library(IRanges)
library(mixtools)
library(data.table)
data(edmr)

# fitting the bimodal normal distribution to CpGs distribution
myMixmdl=myDiff.to.mixmdl(myDiff, plot=T, main="example")

# plot cost function and the determined distance cutoff
plotCost(myMixmdl, main="cost function")

# calculate all DMRs candidate
mydmr=edmr(myDiff, mode=1, ACF=TRUE)

# further filtering the DMRs
mysigdmr=filter.dmr(mydmr)

## annotation
# get genebody annotation GRangesList object
#genebody=genebody.anno(file="http://edmr.googlecode.com/files/hg19_refseq_all_types.bed")
genebody.file=system.file("extdata", "chr22.hg19_refseq_all_types.bed.gz", package = "edmr")
genebody=genebody.anno(file=genebody.file)

# plot the eDMR genebody annotation
plotdmrdistr(mysigdmr, genebody)

# get CpG islands and shores annotation
#cpgi=cpgi.anno(file="http://edmr.googlecode.com/files/hg19_cpgisland_all.bed")
cpgi.file=system.file("extdata", "chr22.hg19_cpgisland_all.bed.gz", package = "edmr")
cpgi=cpgi.anno(file=cpgi.file)

# plot the eDMR CpG islands and shores annotation
plotdmrdistr(mysigdmr, cpgi)

# prepare genes for pathway analysis with significant DMRs at its promoter regions 
dmr.genes=get.dmr.genes(myDMR=mysigdmr, subject=genebody$promoter, id.type="gene.symbol")
dmr.genes