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
Creation and usage: It can be constructed from a numeric matrix of ratios aligned to a set
Applications: GenomicRatioSet is widely used in methylation data analyses, including Illumina methylation arrays and sequencing-based methylation
Notes: Details of slots and inheritance can vary by Bioconductor version, but the core idea remains: coupling