Mapping between UCSC and Ensembl Genome Builds

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Description

genomeBuilds lists the available genomes for a given species while mapGenomeBuilds maps between UCSC and Ensemble genome builds.

Usage

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genomeBuilds(organism, style = c("UCSC", "Ensembl"))

mapGenomeBuilds(genome, style = c("UCSC", "Ensembl"))

listOrganisms()

Arguments

organism

A character vector of common names or organism

genome

A character vector of genomes equivalent to UCSC version or Ensembl Assemblies

style

A single value equivalent to "UCSC" or "Ensembl" specifying the output genome

Details

genomeBuilds lists the currently available genomes for a given list of organisms. The genomes can be shown as "UCSC" or "Ensembl" IDs determined by style. organism must be specified as a character vector and match common names (i.e "Dog", "Mouse") or organism name (i.e "Homo sapiens", "Mus musculus") . A list of available organisms can be shown using listOrganisms().

mapGenomeBuilds provides a mapping between "UCSC" builds and "Ensembl" builds. genome must be specified as a character vector and match either a "UCSC" ID or an "Ensembl" Id. genomeBuilds can be used to get a list of available build Ids for a given organism. NA's may be present in the output. This would occur when the current genome build removed a previously defined genome for an organism.

In both functions, if style is not specified, "UCSC" is used as default.

Value

A data.frame of builds for a given organism or genome in the specified style. If style == "UCSC", ucscID, ucscDate and ensemblID are given. If style == "Ensembl", ensemblID, ensemblVersion, ensemblDate, and ucscID are given. The opposing ID is given so that it is possible to distinguish between many-to-one mappings.

Author(s)

Valerie Obenchain Valerie.Obenchain@roswellpark.org and Lori Shepherd Lori.Shepherd@roswellpark.org

References

UCSC genome builds https://genome.ucsc.edu/FAQ/FAQreleases.html Ensembl genome builds http://useast.ensembl.org/info/website/archives/assembly.html

Examples

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listOrganisms()

genomeBuilds("mouse")
genomeBuilds(c("Mouse", "dog", "human"), style="Ensembl")

mapGenomeBuilds(c("canFam3", "GRCm38", "mm9"))
mapGenomeBuilds(c("canFam3", "GRCm38", "mm9"), style="Ensembl")