[Bioc-devel] Passing packages as variables?

Charles Plessy charles-listes+bioc-devel at plessy.org
Sun Jun 11 02:56:50 CEST 2017

Le Sat, Jun 10, 2017 at 03:11:37PM -0400, Zach Skidmore a écrit :
> genome <- findCorrectGenome()
> library(genome, character.only=T)
> refBases <- getSeq(genome, Granges)
> detach(genome, unload = T, character.only = T)
> It feels wrong to have library calls like this within the package though. As
> an alternative I suppose I could put in the suggests field all BSgenome
> packages, but I don't really want to do that either. does any one have a
> better idea? I think the ideal solution would be to just do something like
> this:
> refBases <- getSeq(geome::genome, Granges)

Hello Zach,

recently, I did something like this:

genome <- getExportedValue(genome, genome)

I am not sure if it is the best solution, but for the moment, it works.

Have a nice week-end,


Charles Plessy, Ph.D. – RIKEN Center for Life Science Technologies
Division of Genomic Technologies – Genomics Miniaturization Technology Unit
1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
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