This is also exciting when one is working on a BigMatrix :-)

Perhaps the default could, at some point, become FALSE when the matrix is
not being subsetted?  Or... I don't know.
I do know that this, and cbind()'ing BigMatrix objects to add new samples,
has been somewhat interesting in my work.




On Tue, Jul 9, 2013 at 3:34 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> The problem is that the dimnames are stored in only one location, and this
> is not on the assays. When you ask for the assays, the dimnames are added,
> triggering a full copy of the data. If the dimnames are not of interest,
> then
>
>   assays(BS, withDimnames=FALSE)
>
> This is not really ideal, so I'll give some thought to a better
> implementation.
>
> Martin
> ----- Kasper Daniel Hansen <kasperdanielhansen@gmail.com> wrote:
> > 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@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
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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