getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
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Aditya ▴ 120
@aditya-7667
Last seen 6 months ago
Germany

Is there a way to avoid BiocGenerics, S4Vectors, IRanges, and Biostrings from being attached when calling BSgenome::getBSgenome() ?

bsgenome <- BSgenome::getBSgenome('mm10')

Attaching package: ‘BiocGenerics’
    The following objects are masked from ‘package:parallel’:
        clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, 
        clusterExport, clusterMap, parApply, parCapply, 
        parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
    The following objects are masked from ‘package:stats’:
        IQR, mad, sd, var, xtabs
    The following objects are masked from ‘package:base’:
        anyDuplicated, append, as.data.frame, basename, 
        cbind, colnames, dirname, do.call, duplicated, eval, 
        evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, 
        lapply, Map, mapply, match, mget, order, paste, pmax, 
        pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, 
        rownames, sapply, setdiff, sort, table, tapply,
        union, unique, unsplit, which, which.max, which.min

Attaching package: ‘S4Vectors’
    The following object is masked from ‘package:base’:
        expand.grid

Attaching package: ‘IRanges’
    The following object is masked from ‘package:grDevices’:
        windows

Attaching package: ‘Biostrings’
    The following object is masked from ‘package:base’:
        strsplit
BSgenome Bsgenome.Mmusculus.UCSC.mm10 • 367 views
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This works, but relies on using (BioC non-complyingly) non-exported functionality - can this be done better?

bsname <- BSgenome:::.getInstalledPkgnameFromProviderVersion('mm10')
bsgenome <- utils::getFromNamespace(bsname, bsname)
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Entering edit mode
Aditya ▴ 120
@aditya-7667
Last seen 6 months ago
Germany

Solved by Herve Pages in BSgenome 1.53.2 through a new argument load.only Now it can be used without attaching the BSgenome namespace:

BSgenome::getBSgenome(load.only = TRUE)

I must add here that I recently realized that the apparent namespace clashes are actually intentional promotions of primitives and S3 generics to S4 generics, and not something to worry about.

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