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
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