Version Compatibility

Reference examples tested with: GenomicRanges 1.54+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

DMR Detection

"Find differentially methylated regions" → Identify contiguous genomic regions with statistically significant methylation differences between conditions using tiling, smoothing, or kernel-based approaches.

• R: methylKit::tileMethylCounts() + calculateDiffMeth(), bsseq::BSmooth(), DMRcate::dmrcate()

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)

# Get significant DMRs
dmrs <- getMethylDiff(diff_tiles, difference = 25, qvalue = 0.01)
dmrs_hyper <- getMethylDiff(diff_tiles, difference = 25, qvalue = 0.01, type = 'hyper')
dmrs_hypo <- getMethylDiff(diff_tiles, difference = 25, qvalue = 0.01, type = 'hypo')

bsseq BSmooth DMRs

library(bsseq)

# Read Bismark cytosine reports
bs <- read.bismark(files = c('sample1.CpG_report.txt.gz', 'sample2.CpG_report.txt.gz'),
                    sampleNames = c('ctrl', 'treat'),
                    rmZeroCov = TRUE,
                    strandCollapse = TRUE)

# Smooth methylation data
bs_smooth <- BSmooth(bs, mc.cores = 4, verbose = TRUE)

# Filter by coverage
bs_cov <- getCoverage(bs_smooth)
keep <- which(rowSums(bs_cov >= 2) == ncol(bs_cov))
bs_filt <- bs_smooth[keep, ]

# Find DMRs with BSmooth
dmrs_bsseq <- dmrFinder(bs_filt, cutoff = c(-0.1, 0.1), stat = 'tstat.corrected')