Abstract
DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation,
cellular specification and cancer development. Here, we describe an R package, methylKit, that
rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and
hydroxymethylation sequencing experiments. methylKit includes functions for clustering, sample
quality visualization, differential methylation analysis and annotation features, thus automating
and simplifying many of the steps for discerning statistically significant bases or regions of DNA
methylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statistically
significant regions of differential methylation and stratify tumor subtypes. methylKit is available
at
http://code.google.com/p/methylkit
.
