The SummarizedExperiment class also stores metadata on the rows and columns. Metadata on the samples usually include experimental or observational covariates as well as technical information such as processing dates or batches, file paths, etc. Row metadata comprise the start and end coordinates of each feature and the identifier of the containing polymer, for example, the chromosome name. Further information can be inserted, such as gene or exon identifiers, references to external databases, reagents, functional classifications of the region (e.g., from efforts such as the Encyclopedia of DNA Elements (ENCODE) [5]) or genetic associations (e.g., from genome-wide association studies, the study of rare diseases, or cancer genetics). The row metadata aid integrative analysis, for example, when matching two experiments according to overlap of genomic regions of interest. Tight coupling of metadata with the data reduces opportunities for clerical errors during reordering or subsetting operations.
