Smoothing of methylation signal within windows

Question

[franc.jian]

Dear all,

I would like to perform smoothing on my RRBS methylation data using a sliding window approach. Moreover, I would like also to compute the median beta for a series of fixed regions.

I can easily create a bed file for both the regions I am interested in, and for the position of each CpG covered, as my data are in the form of a matrix with CpG coordinates in rows and samples in columns.

I suspect this can be achieved with two different GRanges objects (one for sites and one for regions) and then the findOverlaps() funtion, but I feel like there should be a more elegant solution, maybe using specific packages or a tool that I currently don't know.

Thank you for your help,

Gian

[Friederike]

What's your ultimate goal and which packages have you looked at already?

[franc.jian]

My ultimate goal is to evaluate the median Beta inside specific regions and more generally perform smoothing on methylation data (in the form of a Beta table). To this moment, I managed to obtain a solution using GRanges package, which made sense but was actually a bit intricate!

[Kevin Blighe]

Would you mind posting the solution as an answer (and then accepting your own answer)? May help others.