[Bioc-devel] SummarizedExperiments

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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