Mapping between UCSC and Ensembl Genome Builds
genomeBuilds lists the available genomes for a given
species while mapGenomeBuilds maps between UCSC and Ensemble
genome builds.
genomeBuilds(organism, style = c("UCSC", "Ensembl"))
mapGenomeBuilds(genome, style = c("UCSC", "Ensembl"))
listOrganisms()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 |
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.
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.
Valerie Obenchain Valerie.Obenchain@roswellpark.org and Lori Shepherd Lori.Shepherd@roswellpark.org
UCSC genome builds https://genome.ucsc.edu/FAQ/FAQreleases.html Ensembl genome builds http://useast.ensembl.org/info/website/archives/assembly.html
listOrganisms()
genomeBuilds("mouse")
genomeBuilds(c("Mouse", "dog", "human"), style="Ensembl")
mapGenomeBuilds(c("canFam3", "GRCm38", "mm9"))
mapGenomeBuilds(c("canFam3", "GRCm38", "mm9"), style="Ensembl")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.