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
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
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