Fetch the current genome build (assembly) version from online resources.
Usage
currentEnsemblGenomeBuild(organism)
currentGencodeGenomeBuild(organism)
currentRefseqGenomeBuild(organism, taxonomicGroup = NULL)
currentUcscGenomeBuild(organism)
Arguments
- organism
character(1)
. Full Latin organism name (e.g."Homo sapiens"
).- taxonomicGroup
character(1)
. Only applies to RefSeq. FTP server taxonomic group subdirectory path (e.g. "vertebrate_mammalian"). Defining this manually avoids having to query the FTP server.
Examples
## Ensembl.
try({
currentEnsemblGenomeBuild("Homo sapiens")
currentEnsemblGenomeBuild("Mus musculus")
})
#> [1] "GRCm39"
## GENCODE.
try({
currentGencodeGenomeBuild("Homo sapiens")
currentGencodeGenomeBuild("Mus musculus")
})
#> [1] "GRCm39"
## RefSeq.
try({
currentRefseqGenomeBuild(
organism = "Homo sapiens",
taxonomicGroup = "vertebrate_mammalian"
)
currentRefseqGenomeBuild(
organism = "Mus musculus",
taxonomicGroup = "vertebrate_mammalian"
)
})
#> [1] "GCF_000001635.27_GRCm39"
## UCSC.
try({
currentUcscGenomeBuild("Homo sapiens")
currentUcscGenomeBuild("Mus musculus")
})
#> [1] "mm39"