MethylSet

MethylSet is a Bioconductor S4 class used to store DNA methylation assay data, particularly from Illumina Infinium arrays. It serves as a container for the methylated and unmethylated signal intensities measured for each CpG probe across multiple samples, along with comprehensive metadata describing samples and experiments. The class is primarily associated with the minfi package, which provides preprocessing and analysis workflows for methylation data. MethylSet objects are commonly used as the foundational data structure in downstream analyses such as normalization, quality control, and transformation to derived methylation metrics.

In terms of structure, a MethylSet includes assay data matrices for the two signal channels—methylated (M) and unmethylated (U) intensities—arranged with probes as rows and samples as columns. It also carries sample-level metadata (pData) describing covariates like cohort, treatment, or batch, and dataset-level metadata (experimentData) with information about the study and array platform. Some workflows extend MethylSet to GenomicMethylSet, which adds genomic coordinates and reference annotations to the probes, enabling coordinate-based analyses and integration with other genomic data.

Typical usage involves creating a MethylSet from raw array data after initial preprocessing, followed by computation of methylation metrics (such as beta-values or M-values), quality control, normalization, and downstream analyses like differential methylation testing. Accessor methods provide convenient retrieval of M, U, and metadata, supporting integration with broader Bioconductor workflows. MethylSet thus provides a standardized, interoperable container for Illumina methylation data within a reproducible analysis framework.