7 weeks ago by
Guy's Hospital, London
There is no standard package for this, of course. It will take some effort on your part.
- download the normalised β (beta) methylation values from GEO. You
will know that they are β values because the distribution will go
from 0.0 to 1.0. Most methylation data on GEO in the series matrix
files should be normalised. There is usually an automated R script
that you can use, too. From the main accession page, click on the
Analyze with GEO2R button
- download promoter regions as a BED file - you will have to define what is a promoter in your study. Generally, there is no clear definition of what is a promoter, but activity of H3K27ac, H3K4me1, and H3K27me3 are observed at promoters (and enhancers). You can download information for these from the ChromHMM study (do a search). My preference, however, would be to take the data from FANTOM5, a study from Japan whose aim was to define promoter regions.
- summarise methylation by mean across your promoter regions. For this in R, you can use GenomicRanges
Edit based on noorpratap's comment: it is highly likely that the methylation array already has many probes that target promoter regions. Thus, why not just use these? Check the array platform and then try to obtain the associated annotation / metadata associated with this.