[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
Ume? Plant Science Center

Tel: +46 90 786 5478
Email: nicolas.delhomme at umu.se
SLU - Ume? universitet
Ume? S-901 87 Sweden
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