seqinfo

Seqinfo is an S4 class in the Bioconductor project, primarily used within the GenomicRanges framework to store metadata about the reference sequences in a genome. It provides a single, centralized source of per-sequence information that is attached to genomic ranges objects, enabling consistent coordinate handling across datasets. The class is commonly referred to by its constructor, Seqinfo, and is sometimes described in the context of the seqinfo slot or accessors for sequence metadata.

The Seqinfo object captures key properties of each sequence, including its length, whether the sequence is circular, and the genome assembly name. The main components typically stored are seqlengths (a named vector of sequence lengths), isCircular (a named logical vector indicating circularity), and genome (an optional string naming the genome assembly). This combination allows downstream operations to perform coordinate arithmetic, validation, and visualization with reference to the correct genomic context.

Creating and using Seqinfo is straightforward. A Seqinfo object can be constructed with given seqlengths, isCircular, and genome values, for example Seqinfo(seqlengths = c(chr1 = 1e7, chr2 = 5e6), isCircular = c(chr1 = FALSE, chr2 = FALSE), genome = "hg19"). A GenomicRanges object, such as a GRanges, can carry this metadata via seqinfo(gr) or seqinfo(gr) <- Seqinfo(...). Accessing the information is done through seqinfo(gr) to obtain the Seqinfo object, from which seqlengths(seqinfo(gr)), isCircular(seqinfo(gr)), and genome(seqinfo(gr)) provide the individual properties.

Seqinfo plays a critical role in ensuring that genomic ranges operations—such as subsetting, joining, and coordinate transforms—remain consistent with the reference genome and its annotations. It is a foundational element in the interoperability of genomic data within Bioconductor.