domains / families / science / methylkit-analysis

methylkit-analysis

separate

Imports Bismark coverage or cytosine-report files into the methylKit object model, then runs the import-to-results spine - filterByCoverage, normalizeCoverage, unite/destrand, calculateDiffMeth, getMethylDiff - for both per-CpG (DMC) and fixed-tile (DMR) differential methylation, plus tileMethylCounts, PCA/correlation/clustering QC, and assocComp/removeComp batch handling. Covers the silent default traps that shape the false-positive rate: overdispersion='none' does no correction while 'MN' forces the F-test (ignoring test='Chisq'), adjust defaults to SLIM not BH, getMethylDiff defaults difference=25/qvalue=0.01, cov.bases=0 admits single-CpG tiles, and pool destroys biological replication. Use when importing bisulfite count tables, filtering/normalizing/uniting methylation samples, running methylKit differential testing, or QC-ing methylomes. For per-site test-choice (count vs continuous) see differential-cpg-testing; for selection-aware region FDR (dmrseq/DSS) see dmr-detection.

When to use

• importing bisulfite count tables
• filtering and normalizing methylation samples
• running methylKit differential testing
• QC-ing methylomes
• per-CpG differential methylation
• fixed-tile differential methylation
• tileMethylCounts
• PCA/correlation/clustering QC

When not to use

• per-site test-choice (count vs continuous)
• selection-aware region FDR (dmrseq/DSS)
• long-read MM/ML modBAM input

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