GenomeDescription objects

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Description

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

Details

In general the user will not need to manipulate directly a GenomeDescription instance but will manipulate instead a higher-level object that belongs to a class that extends the GenomeDescription class. For example, the top-level object defined in any BSgenome data package is a BSgenome object and the BSgenome class contains the GenomeDescription class. Thus a BSgenome object is also a GenomeDescription object and can therefore be treated as such. In other words all the methods described below will work on it.

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...

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

providerVersion(x): Return the provider-side version of this genome. For example UCSC uses versions "hg18", "hg17", etc... for the different Builds of the Human genome.

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

releaseName(x): Return the release name of this genome, which is generally 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".

bsgenomeName(x): Uses the meta information stored in x to make 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). Of course 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. Pag├Ęs

See Also

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

  • The Seqinfo class.

Examples

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library(BSgenome.Celegans.UCSC.ce2)
class(Celegans)
is(Celegans, "GenomeDescription")
provider(Celegans)
seqinfo(Celegans)
gendesc <- as(Celegans, "GenomeDescription")
class(gendesc)
gendesc
provider(gendesc)
seqinfo(gendesc)
bsgenomeName(gendesc)