I'm working with some RRBS data that was produced using Zymo's Methyl-MiniSeq service. I'm using R package methylKit to analyze the data which allows me to select specific regions of the genome and measure the degree of methylation which is returned as a percentage. I want to compare my data to some research that has has been done using MethyLight assay in which they defined the degree of methylation as PMR - essentially they counted the number of methylated bases in the sample to a reference that was expected to be completely methylated and used those two numbers to compute a percentage.
To me, it seems that the Percent Methylation values methylKit returns (number of methylated bases / coverage x 100) should be equivalent to PMR for the purpose of defining CIMP-status with a gene panel. Am I overlooking something?
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