GenomeDescription-class: GenomeDescription objects

In GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Description

A GenomeDescription object holds the meta information describing a given genome.

Constructor

Even though a constructor function is provided (GenomeDescription()), it is rarely needed GenomeDescription objects are typically obtained by coercing a BSgenome object to GenomeDescription. This has the effect of stripping the sequences from the object and retaining only the meta information that describes the genome. See the Examples section below for an example.

Accessor methods

In the code snippets below, object or x is a GenomeDescription object.

organism(object): Return the scientific name of the organism of the genome e.g. "Homo sapiens", "Mus musculus", "Caenorhabditis elegans", etc...

commonName(object): Return the common name of the organism of the genome e.g. "Human", "Mouse", "Worm", etc...

providerVersion(x): Return the name of the genome. This is typically the name of an NCBI assembly (e.g. GRCh38.p12, WBcel235, TAIR10.1, ARS-UCD1.2, etc...) or UCSC genome (e.g. hg38, bosTau9, galGal6, ce11, etc...).

provider(x): Return the provider of this genome e.g. "UCSC", "BDGP", "FlyBase", etc...

releaseDate(x): Return the release date of this genome e.g. "Mar. 2006".

releaseName(x): IMPORTANT NOTE: The releaseName() methods for GenomeDescription and BSgenome objects are deprecated in BioC 3.12!

If x is a GenomeDescription object, releaseName(x) returns the release name of this genome, which is usually made of the name of the organization who assembled it plus its Build version. For example, UCSC uses "hg18" for the version of the Human genome corresponding to the Build 36.1 from NCBI hence the release name for this genome is "NCBI Build 36.1".

If x is a BSgenome object, releaseName(x) returns NA_character_.

bsgenomeName(x): Uses the meta information stored in GenomeDescription object x to construct the name of the corresponding BSgenome data package (see the available.genomes function in the BSgenome package for details about the naming scheme used for those packages). Note that there is no guarantee that a package with that name actually exists.

seqinfo(x)

Gets information about the genome sequences. This information is returned in a Seqinfo object. Each part of the information can be retrieved separately with seqnames(x), seqlengths(x), and isCircular(x), respectively, as described below.

seqnames(x)

Gets the names of the genome sequences. seqnames(x) is equivalent to seqnames(seqinfo(x)).

seqlengths(x)

Gets the lengths of the genome sequences. seqlengths(x) is equivalent to seqlengths(seqinfo(x)).

isCircular(x)

Returns the circularity flags of the genome sequences. isCircular(x) is equivalent to isCircular(seqinfo(x)).

Author(s)

H. Pagès

See Also

• The available.genomes function and the BSgenome class in the BSgenome package.

• The Seqinfo class.

Examples

library(BSgenome.Celegans.UCSC.ce2)
BSgenome.Celegans.UCSC.ce2
as(BSgenome.Celegans.UCSC.ce2, "GenomeDescription")

GenomeInfoDb documentation built on April 9, 2021, 6 p.m.