[Bioc-devel] Hsapiens in bioconductor
Hi Tomasz, The name of the BSgenome object defined in a BSgenome data package is the name of the package itself. Hsapiens is just an convenient "alias" for the long name. So you could do: importFrom(BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19) importFrom(BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38) and there should be no more 'R CMD check' warning. Then you need to use the long name in your code to refer to the object. Hope this help, H.
On 09/14/2017 06:14 AM, Tomasz Stokowy wrote:
Dear bioc-devel, I would like to import Hsapiens objects from both BSgenome.Hsapiens.UCSC.hg19 and BSgenome.Hsapiens.UCSC.hg38 this is currently handled in the namespace of my package by import(BSgenome.Hsapiens.UCSC.hg19) import(BSgenome.Hsapiens.UCSC.hg38) I get warning (because I assign two different genomes to Hsapiens variable): Warning: replacing previous import ?BSgenome.Hsapiens.UCSC.hg19::Hsapiens? by ?BSgenome.Hsapiens.UCSC.hg38::Hsapiens? when loading ?RareVariantVis? Could you suggest how to avoid this warning? I would like to use both hg19 and hg38 references in my package. Packages are listed in my Description file under Imports:. Furthermore, I use them as BSgenome.Hsapiens.UCSC.hg38::Hsapiens in my code. Kind regards,
Herv? Pag?s 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 h E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319