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

[Rainer Johannes]

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 <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