DMRcate-package: Illumina 450K methylation array spatial analysis

In timpeters82/DMRcate-release: Illumina 450K methylation array spatial analysis methods

Description

De novo identification and extraction of differentially methylated regions (DMR) in the human genome using 450k array 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 bedGraph generation, GRanges generation and plotting functions.

Author(s)

Tim J. Peters <[e-mail]>

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(myMs.noSNPs, analysis.type="differential",
    design=design, coef=39)
dmrcoutput <- dmrcate(myannotation, lambda=1000)
makeBedgraphs(dmrcoutput=dmrcoutput, betas=myBetas, samps=c(1,39))
phen.col <- c(rep("orange", 38), rep("blue", 38))
DMR.plot(dmrcoutput=dmrcoutput, dmr=1, betas=myBetas, phen.col=phen.col,
    pch=16, toscale=TRUE, plotmedians=TRUE)

timpeters82/DMRcate-release documentation built on May 31, 2019, 2:29 p.m.