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 was confusing. The new
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 was confusing. The new implementation
> still supports unidimension
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
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] >=
It totally makes sense for a matrix to be a vector. But it's a whole
other thing for a SummarizedExperiment to be a Vector. It could be
made to work, but I sort of doubt there is much consistency right now.
Perhaps I'm wrong.
On Tue, Dec 15, 2015 at 11:15 AM, Vincent Carey
wrote:
> perhaps the an
perhaps the answer has to reflect
> is(matrix(), "vector")
[1] TRUE
On Tue, Dec 15, 2015 at 2:05 PM, Michael Lawrence wrote:
> 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 supp
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
___
Bioc-dev
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
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
wrote:
> OK, the
OK, the modifications are in the repositories:
https://github.com/jotsetung/biovizBase
https://github.com/jotsetung/ggbio
let me know if I can be of any help.
cheers, jo
On 14 Dec 2015, at 16:00, Rainer Johannes
mailto:johannes.rai...@eurac.edu>> wrote:
I’ll do, thanks for all comments!
On
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