getGenome: getGenome

Description Usage Arguments Details Value Note See Also Examples


Function to obtain a genome





The genome object or genome identifier.


If genome is a BSgenome (from the package BioStrings), it will transform it into a GRanges with chromosomes and chromosome lengths.

If genome is a data.frame with 3 columns, it will transform it into a GRanges.

If genome is a data.frame with 2 columns, it will assume the first is the chromosome, the second is the length of the chromosomes and will add 1 as start.

If genome is a character string uniquely identifying a BSgenome installed in the system (e.g. "hg19", "mm10",... but not "hg"), it will create a genome based on the BSgenome object identified by the character string.

If genome is a GRanges object, it will return it as is.

If genome is non of the above, it will give a warning and try to transform it into a GRanges using toGRanges. This can be helpful if genome is a connection to a file.


A GRanges object with the "genome" data c(Chromosome, Start (by default, 1), Chromosome Length) given a BSgenome, a genome name, a data.frame or a GRanges.

A GRanges representing the genome with one region per chromosome.


This function is memoised (cached) using the memoise package. To empty the cache, use forget(getGenome)

Please note that passing this function the path to a file will not work, since it will assume the character is the identifier of a genome. To read the genome from a file, please use getGenome(toGRanges("path/to/file"))

See Also

getMask, getGenomeAndMask, characterToBSGenome, maskFromBSGenome, emptyCacheRegioneR



getGenome(data.frame(c("chrA", "chrB"), c(15000000, 10000000)))

Search within the regioneR package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.