[Bioc-devel] SummarizedExperiments

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Thu Aug 30 06:52:20 CEST 2012

On Thu, Aug 30, 2012 at 12:44 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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

Yes, for example manipulating colData - something that conceptually
should be quick and easy.  Of course, this will not affect any real
computation on the assayData matrices, but it will make life at the
command prompt more pleasant.


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