[Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

[Rainer Johannes]

Dear all,

I’m having hard times to extend the extractTranscriptSeqs method implemented in GenomicFeatures. Basically, I would like to implement a method for signature(x="ANY”, transcripts="EnsDb”), so that I can re-use the method from GenomicFeatures and add the optional parameter “filter” which would allow to further specify from which transcripts the sequence should be returned.
The problem is that when I try e.g. to define a extractTranscrptSeqs method with transcripts being an EnsDb object:

setMethod("extractTranscriptSeqs",
          signature(x="ANY", transcripts="EnsDb"),
          function(x, transcripts, filter){
              return(extractTranscriptSeqs(x, transcripts, filter=list()))
          })


I get the error:

** preparing package for lazy loading
Error in match.call(definition, call, expand.dots, envir) : 
  unused argument (transcripts = c("EnsDb", "ensembldb"))
Error : unable to load R code in package ‘ensembldb’

It would make life easier for me, if the generic in GenomicFeatures would be defined as:

setGeneric("extractTranscriptSeqs",
    function(x, transcripts, ...) standardGeneric("extractTranscriptSeqs")
)
Instead of

setGeneric("extractTranscriptSeqs", signature="x",
    function(x, transcripts, ...) standardGeneric("extractTranscriptSeqs")
)

Since that seems to solve my problem. There might however also be an alternative solution which I’m not aware of.

Thanks for help or any alternative solutions!

jo