[Bioc-devel] SummarizedExperiment initialisation and manipulation question.

[Hervé Pagès]

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