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dmr-detection

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Detects differentially methylated regions (DMRs) from short-read bisulfite (WGBS/RRBS), array, and long-read methylation count tables using dmrseq (permutation region-FDR over the region selection), DSS callDMR (beta-binomial), methylKit tiles, bsseq BSmooth, DMRcate Gaussian-kernel smoothing, metilene, and comb-p. Covers why a DMR is DEFINED by arbitrary thresholds (min-CpGs, max-gap, delta-beta, q) and a smoothing bandwidth, why selecting extreme runs of CpGs then testing them on the same data is post-selection inference, why region q-values are not comparable across tools, and a single-sample domain-segmentation section (PMD, UMR/LMR, MethylSeekR, solo-WCGW) that must run before focal calling on cancer/aging genomes. Use when calling region-level methylation differences, choosing a DMR caller, controlling region-level FDR, or segmenting megabase methylation domains. For per-site testing see differential-cpg-testing; for the methylKit object model see methylkit-analysis.

When to use

• calling region-level methylation differences
• choosing a DMR caller
• controlling region-level FDR
• segmenting megabase methylation domains
• detecting DMRs from WGBS/RRBS counts
• detecting DMRs from array beta/M
• detecting DMRs from long-read modkit bedMethyl
• single-sample domain segmentation

When not to use

• per-site DMC/DMP testing
• methylKit object model
• long-read MM/ML calling
• functional enrichment of DMR genes

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