[Bioc-devel] SummarizedExperiment initialisation and manipulation question.

[Nicolas Delhomme]

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.delhomme at umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---------------------------------------------------------------

> On 30 Jun 2015, at 07:56, Hervé Pagès <hpages at fredhutch.org> 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.delhomme at umu.se
>>> SLU - Umeå universitet
>>> Umeå S-901 87 Sweden
>>> ---------------------------------------------------------------
>>> 
>>> _______________________________________________
>>> 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