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. Cheers, H. 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel