How to extract gene level methylation values?

I used Bismark to align BS-Seq data followed by methylKit for differential methylation identification. By default, the analysis considers CpG sites, but by using suitable annotation BED file, we can perform region level (promoters, exons, TSS) analysis. I was wondering how to obtain gene level methylation values?

Hi @ag1805x,

dependent on what you are interested in there may be multiple ways to get gene level values. You may perform a gene-level (aka regional) analysis by using the regionCounts() function to extract a methylRaw/methylRawList object for each region of interest as described here in the vignette and proceed as usual with the downstream analysis. Or if you want to keep the single CpGs statistics you could first run the analysis and then extract CpG sites overlapping your genes of interest using the selectByOverlap() function as described in the vignette. Finally, you could convert your analyzed methylDiff object into a GRanges object and proceed using GenomicRanges functions.

Best, Alex