rowRanges

rowRanges is an accessor used in Bioconductor’s SummarizedExperiment framework to store and access the genomic coordinates of each feature (row) in an experiment. The row ranges are typically represented as a GRanges object, which encodes the chromosome (seqnames), the genomic interval (ranges), and the strand for each feature. The number of ranges in rowRanges should match the number of rows in the assays of the object.

In practice, a RangedSummarizedExperiment or a SummarizedExperiment containing genomic coordinates will have a rowRanges slot that holds the GRanges describing feature coordinates. You can retrieve and assign these coordinates with rowRanges(x) and rowRanges(x) <- granges_object. When constructing such an object, rowRanges can be supplied directly, for example by creating a SummarizedExperiment with rowRanges = gr from a GRanges object. Conversely, you can extract the coordinates after construction with rowRanges(x).

rowRanges serves to link assay data to genomic location information, enabling coordinate-based operations such as overlaps, subsetting by genomic intervals, or integration with annotation resources. It complements rowData, which holds per-feature metadata not tied to coordinates, and colData, which describes samples. Users should ensure consistency, such as matching lengths between rowRanges and the number of rows in the assay matrix, and be aware that non-genomic SummarizedExperiment objects may not provide rowRanges.