Seqlengths

Seqlengths is a metadata vector used in genomic data objects to record the lengths of each sequence in a genome or assembly. It is typically implemented as a named integer vector where names are sequence identifiers (such as chromosome or contig names) and values are their lengths in base pairs. In Bioconductor, seqlengths is part of the Seqinfo object that accompanies genomic ranges and other sequence-aware data structures.

Purpose and usage: seqlengths enables correct handling of genomic coordinates, validation of ranges, and coordinate-based operations across different assemblies. Its presence allows functions to determine whether a given position or range lies within the defined sequence and supports coordinate transformations and subsetting.

Storage and access: For objects like GRanges, the seqinfo slot stores seqlengths; you can access or modify with seqlengths(x) or seqinfo(x). You can set seqlengths directly using seqlengths(object) <- c("chr1"=248956422, "chr2"=242193529, "chr3"=198295559), or replace the Seqinfo with Seqinfo(seqnames, seqlengths, isCircular, genome) depending on your workflow.

Considerations: Ensure the seqlengths vector matches the actual sequences used; missing or incorrect lengths can cause errors in downstream analyses, especially when importing data from different genome builds or when plotting coverage or performing range queries. If a sequence is circular (for example mitochondrial DNA), the isCircular flag may be set in Seqinfo.

Related concepts: Seqinfo, GRanges, GenomicRanges, and other sequence-aware data structures in Bioconductor rely on seqlengths to represent the structure of the analyzed genome.