There are a large number of R packages available for the analysis of DNA methylation data.  In their publication describing the capabilities of RnBeads in Nature Methods, Assenov et al. provide a very helpful Supplemental Table 1 comparing the functionalities of the available tools for both sequencing and microarray based approaches. Below is a snapshot of some of the information included in this extensive table.  The article and this table are now open access and can be viewed here:

Yassen Assenov, Fabian Müller, Pavlo Lutsik, Jörn Walter, Thomas Lengauer & Christoph Bock. Comprehensive analysis of DNA methylation data with RnBeads. Nature Methods 11, 1138–1140 (2014)