Hi Herve, passing down additional arguments to the internal exonsBy, cdsBy, fiveUTRsByTranscript and threeUTRsByTranscript would do it! That would be great, thanks.
cheers, jo > On 02 May 2016, at 07:38, Hervé Pagès <hpa...@fredhutch.org> wrote: > > Hi Johannes, > > We can make transcriptLengths() a generic but isn't the situation > similar to the extractTranscriptSeqs() situation that you brought > in January > (https://stat.ethz.ch/pipermail/bioc-devel/2016-January/008570.html) for > which adding the ellipsis to the argument list of the > function and proper forwarding of the extra arguments did the trick? > In the case of transcriptLengths() the extra arguments would be > forwarded to the internal calls to transcripts(), exonsBy(), cdsBy(), > fiveUTRsByTranscript(), and threeUTRsByTranscript(), and so > transcriptLengths() would work out-of-the-box on EnsDb objects. > Would that work? > > H. > > On 04/30/2016 04:05 AM, Rainer Johannes wrote: >> Dear all, >> >> I was wondering, you think it would be possible to make the transcriptLength >> function in GenomicFeatures a method and export that? Reason is that I have >> also implemented a transcriptLength function (actually presently a method in >> order to allow that to be used for EnsDb and TxDb objects), but this causes >> the warning >> >> The following object is masked from 'package:GenomicFeatures': >> >> transcriptLengths >> >> on package loading. >> >> Just in case, that’s the code from my package: >> >> if(!isGeneric("transcriptLengths")) >> setGeneric("transcriptLengths", function(x, with.cds_len=FALSE, >> with.utr5_len=FALSE, >> with.utr3_len=FALSE, ...) >> standardGeneric("transcriptLengths”)) >> setMethod("transcriptLengths", "EnsDb", function(x, with.cds_len=FALSE, >> with.utr5_len=FALSE, >> with.utr3_len=FALSE, >> filter=list()){ >> return(.transcriptLengths(x, with.cds_len=with.cds_len, >> with.utr5_len=with.utr3_len, >> with.utr3_len=with.utr3_len, filter=filter)) >> }) >> >> >> cheers, 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
