bio-methylation-array-preprocessing - Preprocess Illumina methylation array IDATs
Converts raw Illumina 450K, EPIC, or EPICv2 IDATs into corrected, masked, and normalized beta and M-value matrices.
Tags
Updated: 2026-10-03Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Read raw IDAT pairs
- Correct background and dye bias
- Adjust Type I/II chemistry
- Mask failed probes
- Normalize probe signals
- Generate beta and M matrices
Inputs
- Raw IDAT pairs
- Array version
- Genome build
- Normalization scenario
- Installed package versions
Outputs
- Corrected beta matrix
- M-value matrix
- Masked probe signals
- Array and genome-build metadata
Requirements
- R environment
- sesame or minfi
- Version-matched array annotations
- sesame data cache for sesame
- sesame for EPICv2 processing