Differentially methylated site is technically measured by each probe. However, CpG island within gene promoter is comprised of numerous probes. Do we have a consensus of how to determine the methylation level of CpG island using methylation level of probes within corresponding CpG island?
In my experience, the most common approach to find DMR is to use the
DSS R package to call and merge DML into regions.
DMC/DML (Differential Methylation Cytosine/Loci) is often calculated by comparing the counts of methylated and unmethylated cytosine at one position between samples.
Steps are to first call DMLs with the
callDML() function. Then call DMRs from these first results with
callDMR(). Finally annotate the DMLs or DMRs using a
GFF file. From there you can look for DMR falling into CpG island. Some of the parameters that can be tuned are the minimum region length, minimum number of differential CpG sites, percentage of CpG sites required to be significant. However I have never heard of what would be the standard values for these parameters. It may not be clearly established yet.
So because the process of calling DMLs and DMRs need robust statistical testing, it is suggested to first call the differential methylated states and then annotate it.