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

[Rainer Johannes]

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.Morgan at 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 <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
>> 
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
> 
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