GenomeDescription-class {GenomeInfoDb} | R Documentation

## GenomeDescription objects

### 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. Pagès

### See Also

- The `available.genomes` function and the BSgenome class in the BSgenome package.

- The Seqinfo 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)

[Package GenomeInfoDb version 1.20.0 Index]