DMRcate (version 1.8.6)

DMRcate-package: DMR calling from bisulphite sequencing and Illumina array data

Description

De novo identification and extraction of differentially methylated regions (DMRs) in the human genome using array and sequencing data. DMRcate extracts and annotates differentially methylated regions (DMRs) using an array-bias corrected smoothed estimate. Functions are provided for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.

References

Peters T.J., Buckley M.J., Statham, A., Pidsley R., Samaras K., Lord R.V., Clark S.J. and Molloy P.L. De novo identification of differentially methylated regions in the human genome. Epigenetics & Chromatin 2015, 8:6, doi:10.1186/1756-8935-8-6

Examples

data(dmrcatedata)
myMs <- logit2(myBetas)
myMs.noSNPs <- rmSNPandCH(myMs, dist=2, mafcut=0.05)
patient <- factor(sub("-.*", "", colnames(myMs)))
type <- factor(sub(".*-", "", colnames(myMs)))
design <- model.matrix(~patient + type) 
myannotation <- cpg.annotate("array", myMs.noSNPs, analysis.type="differential",
    design=design, coef=39)
dmrcoutput <- dmrcate(myannotation, lambda=1000, C=2)
results.ranges <- extractRanges(dmrcoutput, genome = "hg19")
groups <- c(Tumour="magenta", Normal="forestgreen")
cols <- groups[as.character(type)]
samps <- c(1:6, 38+(1:6))
DMR.plot(ranges=results.ranges, dmr=1, CpGs=myBetas, phen.col=cols, genome="hg19", samps=samps)