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

On 02 May 2016, at 07:38, Herv? Pag?s <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

-- 
Herv? Pag?s

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

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, Herv? Pag?s <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

-- Herv? Pag?s

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

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, Herv? Pag?s <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

-- Herv? Pag?s

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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