I noticed that MEDIPS doesn't seem to assess alternative methylation contexts like CHG or CHH. This seems to stem from not allowing ambiguous matching within
MEDIPS.getPositions. Using something like
matchPattern('CHG', subject, fixed=F) does seem to work.
I can fork this on Github to add a fix, but I'm not sure how this works for Bioconductor modules (particularly since the Github repo mirror is read-only).