bio-methylation-dmr-detection
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)
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