[Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

Hervé Pagès hpages at fredhutch.org
Tue Jan 19 22:31:07 CET 2016

Hi Jo,

In GenomicFeatures 1.23.18 I've modified the default
"extractTranscriptSeqs" method so it can be called with additional
arguments when the 2nd argument in not a GRangesList object. These
additional arguments then get passed to the internal call to exonsBy().
With this change, the user should be able to use extractTranscriptSeqs()
on an EnsDb object and specify any additional argument that is
accepted by the "exonsBy" method for EnsDb objects.

Let me know if you run into problems with this.


On 01/18/2016 06:46 AM, Rainer Johannes wrote:
> 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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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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