Question: Trying to use BSgenome.Hsapiens.NCBI.GRCh38
gravatar for Hervé Pagès
4.5 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:
Hi Hector, I'm cc'ing the Bioconductor mailing list. Hope you don't mind. On 04/04/2014 04:22 PM, Hector Zenil wrote: > Hi Herv? > > I have installed, the latest versions of R and BiConductor and clite, > etc. But BSgenome.Hsapiens.NCBI.GRCh38 doesn't come in the available > genomes. Is there anything special I should be doing to have access to > it? It's only available in BioC devel and as a source package for now. So if you are on Windows or Mac you need to use type="source" when you do available.genomes() or biocLite(). For example on a Mac with R 3.1.0: > library(BSgenome) > grep("GRCh38", available.genomes(), value=TRUE) character(0) > grep("GRCh38", available.genomes(type="source"), value=TRUE) [1] "BSgenome.Hsapiens.NCBI.GRCh38" Note that in BioC devel, there is a new utility, getBSgenome(), documented in the same man page as available.genomes(), that is the recommended way to lookup a BSgenome object by genome assembly or by full BSgenome package name. If the BSgenome package is not installed, it will tell you exactly how to install it: > getBSgenome("GRCh38") Error in .stopOnAvailablePkg(genome, is.source = TRUE) : BSgenome.Hsapiens.NCBI.GRCh38 package is not currently installed. You first need to install it, which you can do with: library(BiocInstaller) biocLite("BSgenome.Hsapiens.NCBI.GRCh38", type="source") See ?getBSgenome for the details. Cheers, H. > > Thanks and best regards, > > - Hector > > Dr. Hector Zenil > > Unit of Computational Medicine > Karolinska Institute, Stockholm > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at Phone: (206) 667-5791 Fax: (206) 667-1319
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