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)seqnames(x), seqlengths(x), and isCircular(x),
respectively, as described below.
seqnames(x)seqnames(x) is equivalent to seqnames(seqinfo(x)).
seqlengths(x)seqlengths(x) is equivalent to seqlengths(seqinfo(x)).
isCircular(x)isCircular(x) is equivalent to isCircular(seqinfo(x)).
available.genomes function and the
BSgenome class in the BSgenome package.
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)
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