Bio Methylation Differential Cpg

Tests individual CpG sites for differential methylation (DMC/DMP) from bisulfite sequencing counts or array/continuous beta-value matrices. Covers the count-vs-continuous fork that dictates the model, beta-value vs M-value logit (Du 2010), beta-binomial overdispersion count models (DSS, methylKit, MOABS, RADMeth) for sequencing, limma moderated-t on M-values (eBayes trend/robust) for arrays, the bare-beta Welch t-test caveat, coverage-as-precision coupling, delta-beta effect size, BH-FDR with the neighboring-CpG dependence problem, EWAS genome-wide thresholds, and differential variability (DiffVar/iEVORA). Use when comparing per-CpG methylation between groups from WGBS/RR…