GenomeDescription-class: GenomeDescription objects

In Przemol/mirrors-bioc-BSgenome: Infrastructure for Biostrings-based genome data packages

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 containing the GenomeDescription class. For example the top-level object defined in any BSgenome data package is a BSgenome object. But because the BSgenome class contains the GenomeDescription class, it 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, x is a GenomeDescription object.

organism(x): Return the target organism for this genome e.g. "Homo sapiens", "Mus musculus", "Caenorhabditis elegans", etc...

species(x): Return the target species for this 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 available.genomes 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. Pages

See Also

available.genomes, Seqinfo-class, BSgenome-class

Examples

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)

Przemol/mirrors-bioc-BSgenome documentation built on May 8, 2019, 3:46 a.m.