Re: [Bioc-devel] SummarizedExperiment initialisation and manipulation question.
Hi Nico,
It seems reasonable indeed to support rowRanges<- on
SummarizedExperiment0. It might be a little bit surprising for the
user that the setter changes the class of the object but it looks
like a perfectly legit situation for doing so here. Also there are
some precedents:
> x <- 1:5
> x[1] <- "a"
> x
[1] "a" "2" "3" "4" "5"
and:
library(Biostrings)
dna <- DNAString("GGATTAAA")
class(dna) # DNAString
masks(dna) <- Mask(length(dna), 2, 5)
class(dna) # MaskedDNAString
I'll add this, unless someone has a better idea?
Thanks,
H.
On 06/29/2015 03:13 AM, Nicolas Delhomme wrote:
Hej alla!
In the simpleRNASeq function of the easyRNASeq package, I start by instantiating a
SummarizedExperiment object not initially providing the rowRanges. This results in the creation of an
object of the class SummarizedExperiment0. When later, once I have validated the annotation, I try to
extend the rowRanges of my SummarizedExperiment object, I get an error message that
"rowRanges<-" is not implemented for signature "SummarizedExperiment0,
GRangesList".
I'm now wondering if this has been omitted on purpose for SummarizedExperiment0
objects or is not yet implemented. The reason I'm wondering is because there is
the possibility to cast a SummarizedExperiment0 object as a
RangedSummarizedExperiment (which is my current work-around), but I'm wondering
if that's the best way to go.
I don't have access to my Rsession right now, so no sessionInfo(), but I'm
using R3.2.1 on OSX 10.10.3 (Yosemite), and the latest devel packages (updated
today; SummarizedExperiment version is 0.3.0).
Cheers,
Nico
---
Nicolas Delhomme, PhD
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 5478
Email: nicolas.delho...@umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---
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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
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Re: [Bioc-devel] SummarizedExperiment initialisation and manipulation question.
Done in SummarizedExperiment 0.3.2.
Thanks for the feedback,
H.
On 06/29/2015 10:26 PM, Hervé Pagès wrote:
Hi Nico,
It seems reasonable indeed to support rowRanges<- on
SummarizedExperiment0. It might be a little bit surprising for the
user that the setter changes the class of the object but it looks
like a perfectly legit situation for doing so here. Also there are
some precedents:
> x <- 1:5
> x[1] <- "a"
> x
[1] "a" "2" "3" "4" "5"
and:
library(Biostrings)
dna <- DNAString("GGATTAAA")
class(dna) # DNAString
masks(dna) <- Mask(length(dna), 2, 5)
class(dna) # MaskedDNAString
I'll add this, unless someone has a better idea?
Thanks,
H.
On 06/29/2015 03:13 AM, Nicolas Delhomme wrote:
Hej alla!
In the simpleRNASeq function of the easyRNASeq package, I start by
instantiating a SummarizedExperiment object not initially providing
the rowRanges. This results in the creation of an object of the class
SummarizedExperiment0. When later, once I have validated the
annotation, I try to extend the rowRanges of my SummarizedExperiment
object, I get an error message that "rowRanges<-" is not implemented
for signature "SummarizedExperiment0, GRangesList".
I'm now wondering if this has been omitted on purpose for
SummarizedExperiment0 objects or is not yet implemented. The reason
I'm wondering is because there is the possibility to cast a
SummarizedExperiment0 object as a RangedSummarizedExperiment (which is
my current work-around), but I'm wondering if that's the best way to go.
I don't have access to my Rsession right now, so no sessionInfo(), but
I'm using R3.2.1 on OSX 10.10.3 (Yosemite), and the latest devel
packages (updated today; SummarizedExperiment version is 0.3.0).
Cheers,
Nico
---
Nicolas Delhomme, PhD
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 5478
Email: nicolas.delho...@umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---
___
Bioc-devel@r-project.org mailing list
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--
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
___
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Re: [Bioc-devel] SummarizedExperiment initialisation and manipulation question.
Thanks for the quick action :-)
Nico
---
Nicolas Delhomme, PhD
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 5478
Email: nicolas.delho...@umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---
> On 30 Jun 2015, at 07:56, Hervé Pagès wrote:
>
> Done in SummarizedExperiment 0.3.2.
>
> Thanks for the feedback,
> H.
>
> On 06/29/2015 10:26 PM, Hervé Pagès wrote:
>> Hi Nico,
>>
>> It seems reasonable indeed to support rowRanges<- on
>> SummarizedExperiment0. It might be a little bit surprising for the
>> user that the setter changes the class of the object but it looks
>> like a perfectly legit situation for doing so here. Also there are
>> some precedents:
>>
>>> x <- 1:5
>>> x[1] <- "a"
>>> x
>> [1] "a" "2" "3" "4" "5"
>>
>> and:
>>
>> library(Biostrings)
>> dna <- DNAString("GGATTAAA")
>> class(dna) # DNAString
>> masks(dna) <- Mask(length(dna), 2, 5)
>> class(dna) # MaskedDNAString
>>
>> I'll add this, unless someone has a better idea?
>>
>> Thanks,
>> H.
>>
>> On 06/29/2015 03:13 AM, Nicolas Delhomme wrote:
>>> Hej alla!
>>>
>>> In the simpleRNASeq function of the easyRNASeq package, I start by
>>> instantiating a SummarizedExperiment object not initially providing
>>> the rowRanges. This results in the creation of an object of the class
>>> SummarizedExperiment0. When later, once I have validated the
>>> annotation, I try to extend the rowRanges of my SummarizedExperiment
>>> object, I get an error message that "rowRanges<-" is not implemented
>>> for signature "SummarizedExperiment0, GRangesList".
>>>
>>> I'm now wondering if this has been omitted on purpose for
>>> SummarizedExperiment0 objects or is not yet implemented. The reason
>>> I'm wondering is because there is the possibility to cast a
>>> SummarizedExperiment0 object as a RangedSummarizedExperiment (which is
>>> my current work-around), but I'm wondering if that's the best way to go.
>>>
>>> I don't have access to my Rsession right now, so no sessionInfo(), but
>>> I'm using R3.2.1 on OSX 10.10.3 (Yosemite), and the latest devel
>>> packages (updated today; SummarizedExperiment version is 0.3.0).
>>>
>>> Cheers,
>>>
>>> Nico
>>> ---
>>> Nicolas Delhomme, PhD
>>>
>>> The Street Lab
>>> Department of Plant Physiology
>>> Umeå Plant Science Center
>>>
>>> Tel: +46 90 786 5478
>>> Email: nicolas.delho...@umu.se
>>> SLU - Umeå universitet
>>> Umeå S-901 87 Sweden
>>> ---
>>>
>>> ___
>>> 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
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