[Bioc-devel] Passing packages as variables?

Zach Skidmore zskidmor at wustl.edu
Sat Jun 10 21:11:37 CEST 2017

Hi all,

I maintain the GenVisR package. I am currently working on an update to provide support for VEP, the problem is I need to grab the reference sequence for locations in the VEP file. I know how to do this with BSgenome however within the package methods I need to figure out a way to load the genome package to get the references. The problem is this genome package can change based on the information in the VEP header. I could do something like this:

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)

But i have no idea if it's even possible to pass variables as package names like this. As a last resort I could make a user just supply the correct BSgenome object but I would rather GenVisR be nice and use the correct one corresponding to the vep header without any user input if possible. Any help or advice is appreciated!



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