Defining BSgenome -> GRanges S4 coercer without package attaching
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Aditya ▴ 160
@aditya-7667
Last seen 2.4 years ago
Germany

Defining an S4 coercer in my multicrispr package

methods::setAs( "BSgenome", "GRanges", 
            function(from)  from %>% 
                            GenomeInfoDb::seqinfo() %>% 
                            as('GRanges'))

gives this byte compile message:

** byte-compile and prepare package for lazy loading
   in method for 'coerce' with signature '"BSgenome","GRanges"': no definition for class "BSgenome"

Importing the BSgenome class in advance avoids these messages, but attaches many dependency packages:

BSgenome <- methods::getClassDef('BSgenome', package = 'BSgenome')

    Loading required package: BSgenome
    Loading required package: BiocGenerics
    Loading required package: parallel
    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

    Loading required package: S4Vectors
    Loading required package: stats4
    Attaching package: ‘S4Vectors’
        The following object is masked from ‘package:base’: expand.grid

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

    Loading required package: GenomeInfoDb
    Loading required package: GenomicRanges
    Loading required package: Biostrings
    Loading required package: XVector
    Attaching package: ‘Biostrings’
        The following object is masked from ‘package:base’: strsplit

    Loading required package: rtracklayer

Is there a way to define the S4 coercer without attaching these dependencies?

BSgenome methods GenomicRanges • 1.5k views
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Many of your questions are similar and I wonder if it would be better to state what your goal is in avoiding 'attaching' packages. Also, it seems like these are related to package development, and the answer for a package developer may well be different from the answer for a user. If these are related to package development, then it is better to ask on the bioc-devel mailing list.

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Thank you Martin :-)

Updated this question to give its full context, and posted to bioc-devel.

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Aditya ▴ 160
@aditya-7667
Last seen 2.4 years ago
Germany

The solution is to use the roxygen keyword @importClassesFrom in the function documentation (thankyou Daniel Kasper Hansen on bioc-devel)

#' Convert BSgenome into GRanges 
#' @param from BSgenome, e.g. BSgenome.Mmusculus.UCSC.mm10::Mmusculus
#' @examples 
#' require(magrittr)
#' bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 
#' as(bsgenome, 'GRanges')
#' @importClassesFrom BSgenome BSgenome
#' @export
methods::setAs("BSgenome", 
               "GRanges", 
               function(from)  as(GenomeInfoDb::seqinfo(from), 'GRanges')

From my recent communications with Herve Pages I have come to understand that these apparant namespace clashes are actually intentional promotions of base primitives and S3 generics to S4 generics. So, not something to worry about.

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