Dear Martin, Lori, I’ve added support for the column “tx_name” (which will return the transcript ID) to all ensembldb methods so that’s fine now. Apparently I was just a little late, since that is now in the devel version 1.5.1.
thanks, jo > On 03 May 2016, at 18:51, Martin Morgan <martin.mor...@roswellpark.org> wrote: > > On 05/02/2016 03:46 AM, Rainer Johannes wrote: >> Hi Herve, >> >> passing down additional arguments to the internal exonsBy, cdsBy, >> fiveUTRsByTranscript and threeUTRsByTranscript would do it! That >> would be great, thanks. > > Hi Johannes -- > > Lori (cc'd, a new team member) and I are working on this. > > The easiest thing to do is add '...' to the transcriptLengths argument list, > and to pass this to transcripts, exonsBy, etc. > > The only obstacle is that 'tx_name' (in the call to transcripts()) plays a > central role in TxDb, but is not supported by EnsDb. Is it reasonable for you > to add support for tx_name as a column (maybe a simple alias to tx_id, so no > need for schema change)? > > Martin & Lori > >> >> 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 >> > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
