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array-qc-filtering

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Performs probe filtering and sample-level QC on Illumina Infinium methylation arrays (450K / EPIC / EPICv2) to decide which probes and samples to trust. Drops detection-p-failed and low-bead-count probes, removes cross-reactive/non-specific probes (Chen 2013 / Pidsley 2016 lists via maxprobes), excludes SNP-overlapping probes with dropLociWithSnps, and handles sex-chromosome probes. Collapses EPICv2 replicate probes with betasCollapseToPfx and harmonizes across array versions (EPICv2 hg38 vs 450K/EPIC hg19, intersect plus mLiftOver). Runs sample-identity QC: getSex sex prediction vs sample sheet for swap detection, rs-SNP fingerprint clustering for duplicates/swaps, and Sentrix chip/array-position batch diagnosis. Use when filtering methylation array probes, detecting sample swaps or mislabels, collapsing EPICv2 replicates, or merging 450K/EPIC/EPICv2 cohorts. For IDAT-to-corrected-beta normalization see array-preprocessing; for batch correction and study design see ewas-design.

When to use

• filtering methylation array probes
• detecting sample swaps or mislabels
• collapsing EPICv2 replicates
• merging 450K/EPIC/EPICv2 cohorts
• removing cross-reactive probes
• excluding SNP-overlapping probes
• sample-identity QC
• cross-version harmonization

When not to use

• IDAT-to-corrected-beta normalization
• batch correction
• study design
• per-CpG testing
• cohort cell-composition QC
• short-read bisulfite sequencing
• long-read MM/ML calling

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