GenomicRatioSet

GenomicRatioSet is an S4 class used in Bioconductor to store genomic coordinate information together with a matrix of genomic ratio measurements across multiple samples. It is commonly employed in epigenomics to represent data such as DNA methylation, where each row corresponds to a genomic feature (for example a CpG probe or genomic region) and each column corresponds to a sample, with an associated ratio value (such as a beta value or M-value).

Structure and representation: A GenomicRatioSet typically stores per-feature coordinates in a rowRanges component (often a GRanges object) and per-sample measurements in one or more assay matrices accessible via the assays slot. Sample metadata is kept in colData, and feature metadata in rowData or related metadata slots. The class integrates genomic coordinates with quantitative measurements, enabling coordinate-aware analyses within the Bioconductor ecosystem.

Creation and usage: It can be constructed from a numeric matrix of ratios aligned to a set of genomic coordinates. Because GenomicRatioSet extends the SummarizedExperiment framework, standard extractors and operations apply, such as assays(), rowRanges(), colData(), and subsetting by rows or columns. Many workflows also provide helper functions to convert between different representations (for example, beta values and M-values) within a GenomicRatioSet.

Applications: GenomicRatioSet is widely used in methylation data analyses, including Illumina methylation arrays and sequencing-based methylation studies. It supports downstream analyses such as differential methylation testing, region-based aggregations, and visualization, while keeping the data anchored to precise genomic coordinates.

Notes: Details of slots and inheritance can vary by Bioconductor version, but the core idea remains: coupling genomic coordinates with a matrix of per-sample ratio measurements in a coherent, coordinate-aware data structure.