mapGenomeBuilds {GenomeInfoDb} | R Documentation

## Mapping between UCSC and Ensembl Genome Builds

### Description

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

### Usage

    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

    listOrganisms()

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

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

[Package GenomeInfoDb version 1.16.0 Index]