On 03/20/2014 06:29 PM, Kasper Daniel Hansen wrote:
It used to be the case that when a SummarizedExperiment was constructed,
dim names was removed from the matrices in assay. One could then either use
(1) assay(, withDimnames = TRUE)
which ensured dim names in the return value, but implied copying of the
return object because the dim names had to get added, or
(2) assay(, withDimnames = FALSE)
which ensured that the return object had no dim names (because they were
stripped).
It seems in a recent commit (based on log message I am guessing the two
copied in at the bottom of the email, dim names are not stripped at
construction. This implies that
assay(, withDimnames = FALSE)
returns an object with the dimnames because they are already present in the
raw object.
Now, my questions are
(1) can I depend on this behavior?
yes.
(2) Is there any check that the dimnames which may be present in the 'raw'
assay object are in line with what I get from assay(withDimnames = TRUE) or
could I imagine getting different dimnames (and not just no dimnames vs
with dimnames) depending on withDimnames?
more structure will be imposed; the dimnames of the overall object will agree
with the dimnames of the assays.
To get some context, in bsseq I always use withDimnames=FALSE because the
assay matrices are big (28M rows), so I want to avoid copying. But now I
get a failed test, since I construct an object with colnames in the assay.
This seems to be an esoteric point, but it has performance implications in
my usage. I don't know what the right design is - I like that renaming
things are quick, because it only happens in the colData slot.
I think stripping the dimnames from assays was a mistake -- it saves space (but
not much compared to the assay data) but causes a performance bottleneck in
normal use (when the dimnames are copied to the assay data) so I think it makes
sense to just duplicate / check dimnames. This is the direction I'll go in,
unless there are other opinions.
Finally, it seems that the NEWS file in GenomicRanges is no longer
maintained. Is this intentional ? :(
the *Ranges tradition seems to be to update the NEWS files prior to release,
rather than during development. So for instance
------------------------------------------------------------------------
r87773 | hpa...@fhcrc.org | 2014-03-24 00:49:50 -0700 (Mon, 24 Mar 2014) | 1
line
start to update NEWS file with changes in the upcoming 1.16.0 version
Best,
Kasper
r77404 | mtmor...@fhcrc.org | 2013-06-11 15:52:25 -0400 (Tue, 11 Jun 2013)
| 5 lines
relax SummarizedExperiment assays class validity
- dim() of length >= 2
- does not guarantee functionality; may be altered in the future
------------------------------------------------------------------------
r76679 | mtmor...@fhcrc.org | 2013-05-16 17:12:43 -0400 (Thu, 16 May 2013)
| 4 lines
more efficient ref class constructor
- new empty instance, the update slots
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