[Bioc-devel] GenomicRanges::assays

Note the final "s" in assays.  It is super slow.  This is a BSseq object
with 28M rows and 7 columns, which means there are two assays M and Cov
each being 28M x 7 (which is pretty big, on the Gb scale)

These two commands retrieve the same data as far as I understand.

system.time({BS at assays$field("data")})

   user  system elapsed
      0       0       0

system.time({assays(BS)})

   user  system elapsed
 19.677  10.436  30.114

Follow up question:

1) It seems that all assays are stored in a SimpleList inside a reference
class.  If I only want to replace one of the assays, like
  assay(Object, "NAME") <- value
does this mean that all assays are being copied?  Is this different from
say eSet where each assay is a matrix in an environment?

2) I think we need a convenience function for the assay names of a
SummarizedExperiment.  (This is how I saw the issue above, I was using
names(assays(Object)))

Kasper

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