Thanks Hervé! I’ll check it out but don’t expect any problems.
cheers, jo > On 19 Jan 2016, at 22:31, Hervé Pagès <hpa...@fredhutch.org> wrote: > > 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