DMR Detection

methylKit Tile-Based DMRs

library(methylKit)

# Read and process data
meth_obj <- methRead(location = file_list, sample.id = sample_ids, treatment = treatment,
                      assembly = 'hg38', pipeline = 'bismarkCoverage')
meth_filt <- filterByCoverage(meth_obj, lo.count = 10, hi.perc = 99.9)

# Create tiles (windows)
tiles <- tileMethylCounts(meth_filt, win.size = 1000, step.size = 1000, cov.bases = 3)

tiles_united <- unite(tiles, destrand = TRUE)

# Differential methylation on tiles
diff_tiles <- calculateDiffMeth(tiles_united, overdispersion = 'MN', mc.cores = 4)