seconded
On Tue, Jul 9, 2013 at 6:33 PM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:
> Especially since it seems that
> assay()
> has no option for dim names and therefore automatically removes them.
>
> I vore for withDimNames = FALSE and also adding the option to assay() (or
> remove it from assays())
>
>
> On Tue, Jul 9, 2013 at 9:06 PM, Kasper Daniel Hansen <
> kasperdanielhan...@gmail.com> wrote:
>
> > Thanks for the answer, which explains the reasoning. I will argue it is
> a
> > design mistake to have withDimNames=TRUE as default as it destroys the
> nice
> > work on not copying the assays. If you want the return object to include
> > dimnames per default I see no other reason than to store them in the
> assays
> > (unlike now where they are stripped), which should not take up much
> memory,
> > but will slow down the replacement methods for colnames and rownames.
> >
> > In the old bsseq I insisted on sampleNames (because they are super
> useful)
> > and on not having rownames (because I have the granges coordinates). Of
> > course, that was just my choice for my application, and I fully
> understand
> > not having dimnames at all.
> >
> > In case the above is super confusing, this is a very strong vote for
> > having withDimNames=FALSE as the default.
> >
> > Kasper
> >
> >
> >
> >
> > On Tue, Jul 9, 2013 at 6:34 PM, Martin Morgan <mtmor...@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 <kasperdanielhan...@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]]
> >> >
> >> > _______________________________________________
> >> > Bioc-devel@r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >>
> >
>
> [[alternative HTML version deleted]]
>
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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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