[Bioc-devel] SummarizedExperiments

Martin Morgan mtmorgan at fhcrc.org
Thu Aug 30 06:44:56 CEST 2012

On 08/29/2012 06:46 PM, Kasper Daniel Hansen wrote:
> There is a lot of good stuff to say about SummarizedExperiments, and
> from a certain point of view I have a parallel implementation in bsseq
> (and there is also one in genoset).
> However, I really like having the assayData inside an environment.
> This helps some on memory and - equally important - speed at the
> command line.  I certainly need to very heavily consider using an
> environment in bsseq.
> After some discussion with Tim (Triche) we have agreed that something
> like SummarizedExperiments is the way to go at least for the
> methylation arrays.  We need to be able to easily handle 1000s of
> samples.
> What is the chance that we can get the option of having the assayData
> inside an environment, perhaps by
>    Making a class that is an environment and inherits from SimpleList.
>    Using a classUnion between the existing class of the assayData and
> an environment.
>    Third option that is probably better than the proceeding two, but
> which I cannot come up with right now.

Probably something can / will be done. I guess the slowness you're 
talking about is when rowData / colData columns are manipulated; any 
kind of subsetting would mean a 'deep' copy. Martin

> This would - in my opinion - be very nice and worthwhile.
> Kasper
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