I am glad to say that new version ChAMP package is already online. New version package has been totally rewrote and designed, there are lots of differences and upgrading compared with old version. Key features includes:
(1): All beta matrix along with pd file can be analysed, the old version can only accept IDAT file as input.
(2): Provide interactive interface and plot to check ChAMP result, you don't need to struggle to plot DMR, DMP, DMB or even heatmap.
(3): Expanded Human Methylation analysis pipeline to Differential Methylation Blocks (DMB) and GSEA analysis.
(4): PPI network analysis on methylation level, detect interactive PPI hot spots.
(5): More methods for normalization and DMR calling are included.
(6): Support EPIC array.
The link of this package is https://www.bioconductor.org/packages/devel/bioc/html/ChAMP.html
You may check the html version of vignette here: https://www.bioconductor.org/packages/devel/bioc/vignettes/ChAMP/inst/doc/ChAMP.html
I am the author and maintainer of ChAMP2, it's a comprehensive and large package, thus I will try my best to avoid bug and correct any potential problems in the future. ^_^. If you find any bug or have any suggestion, please email to ChAMP450K@gmail.com.