[Bioc-devel] what is SummarizedExperiment a Vector of?

Saw that SummarizedExperiment(0) derives from Vector. What exactly is it a Vector of? Features? Measurements? It is rectangular, like a matrix, but does it support unidimensional subscripts? Sort of confusing. Thanks for clarifying, Michael ___

Re: [Bioc-devel] what is SummarizedExperiment a Vector of?

It seems worthy of discussion. My outlook, surely naive, is that SummarizedExperiment is Vector if it can answer all these meaningfully > methods(class="Vector") [1] !=[ [<- %in% [5] < <===> [9]

Re: [Bioc-devel] what is SummarizedExperiment a Vector of?

On 12/15/2015 03:13 PM, Michael Lawrence wrote: On Tue, Dec 15, 2015 at 2:15 PM, Hervé Pagès wrote: SummarizedExperiment has long been supporting unidimensional subsetting which was subsetting by row. However the length of any SE object was always considered to be 1 which

Re: [Bioc-devel] Extending biovizBase and ggbio packages

Great, thanks for this valuable contribution. I made some comments on the commits. The biggest issue is that I think there is a lot of code duplication between the EnsDb and TxDb methods. We should try hard to reduce this. Michael On Tue, Dec 15, 2015 at 1:37 AM, Rainer Johannes

Re: [Bioc-devel] what is SummarizedExperiment a Vector of?

SummarizedExperiment has long been supporting unidimensional subsetting which was subsetting by row. However the length of any SE object was always considered to be 1 which was confusing. The new implementation still supports unidimensional subsetting but now the length of an object is its number

Re: [Bioc-devel] Extending biovizBase and ggbio packages

Thanks for the comments! I’ll make some changes and push a “cleaner” version once I’m done. Indeed, I have to reduce code duplications. I could also use the same or similar code than for TxDb, but I wanted to make as much use of the EnsDb filter system as possible to reduce processing time. jo