[Bioc-devel] Making transcriptLength function a method in GenomicFeatures?

Martin Morgan martin.morgan at roswellpark.org
Tue May 3 18:51:53 CEST 2016

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 <hpages at 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 at 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: hpages at fredhutch.org Phone:  (206) 667-5791 Fax:    (206)
>> 667-1319
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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