The MIRA package aggregates DNA methylation across the genome for instances of a genomic feature like histone ChIP peaks, transcription factor ChIP peaks, or open chromatin regions. MIRA provides a single signature and score for each feature. This lets you use DNA methylation data to infer regulatory activity.
To test enrichments, you need a database. A good place to start is the LOLA Core database, which provides a curated resource of public datasets. Information on both options are in the RegionDB docs.
The development version is maintained on GitHub and can be installed directly from github: