Question: Smoothing of methylation signal within windows
gravatar for franc.jian
22 months ago by
franc.jian40 wrote:

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,


R genome • 549 views
ADD COMMENTlink written 22 months ago by franc.jian40

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

ADD REPLYlink written 22 months ago by Friederike5.7k

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!

ADD REPLYlink written 22 months ago by franc.jian40

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

ADD REPLYlink written 21 months ago by Kevin Blighe61k
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