[Bioc-devel] SummarizedExperiment vs ExpressionSet

On 11/26/2014 12:11 PM, Herv? Pag?s wrote:

Hi guys,

I like the idea of separating the row data from the row ranges.
This could be formalized with 2 distinct accessors: rowData() and
rowRanges(). The former would return a DataFrame, and the latter
NULL or a range-based object (GRanges or GRangesList).
I don't think there is the need for an emptyRanges class.

For the original question, I think the ability to store genomic
coordinates as well as other 'S4Vector' classes is very helpful for
advanced users, even if a little intimidating for novice users.

Also, it's clear that SummarizedExperiment in its current form doesn't
satisfy the common use case of identifiers without range information.

I think it makes sense to enable some like Herve outlines above, where the
rowData() are separated into range information and annotation information,
and I'll move forward with that implementation over the next week or so.

Martin

H.

On 11/26/2014 11:40 AM, Hector Corrada Bravo wrote:

One thing that?s become apparent working on epivizr is that it may be
useful
to think about ?rowData? in a SummarizedExperiment as having two distinct
components: row coordinates and row metadata. In the current class
rowData is
a ?GenomicRanges? which contains both coordinates (the ranges) and
metadata
(mcols(rowData)). In metagenomics (the other application my group works
a lot
with), we think of the taxonomy as providing coordinates. The
distinction is
worthwhile thinking about since there are certain operations we do on
coordinates that we don?t do with metadata (and conversely).




Thinking about it this way, the ?ExpressionSet? object would be data
without
coordinates. So, I would avoid making ?GenomicRanges? behave like
?DataFrame?
since this distinction between coordinates and metadata is lost. The
?emptyRanges? proposal gets closer to this since this corresponds to ?no
coordinates?, but it may be worth thinking in the long term on making the
coordinate/metadata distinction more general.




Hector

On Wed, Nov 26, 2014 at 12:38 PM, Tim Triche, Jr. <tim.triche at gmail.com>
wrote:

 so as a simple experiment, I did the following:

library(GenomicRanges)
bar <- matrix(rnorm(100), ncol=10)
colnames(bar) <- as.character(1:10)
rownames(bar) <- letters[1:10]
foo <- SummarizedExperiment(assays=list(bar=bar))
rowData(foo)
## GRangesList object of length 10:
## $a
## GRanges object with 0 ranges and 0 metadata columns:
##    seqnames    ranges strand
##       <Rle> <IRanges>  <Rle>
##
## $b
## GRanges object with 0 ranges and 0 metadata columns:
##      seqnames ranges strand
##
## $c
## GRanges object with 0 ranges and 0 metadata columns:
##      seqnames ranges strand
##
## ...
## <7 more elements>
colData(foo)
## DataFrame with 10 rows and 0 columns
This got me to thinking, why not have an emptyRanges class, or else the
ability to index a bunch of NULL ranges without a lot of hoohah?  The
defaults mostly do what they're supposed to; why not have a compact
representation of empty rowData as for empty colData (i.e., a DataFrame
with 0 rows)?  Or is a GRangesList of empty GRanges as compact as it is
practicable to get for this purpose?
Just pondering what the lowest-impact solution to the problem at hand
might
be.
Statistics is the grammar of science.
Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
On Wed, Nov 26, 2014 at 9:07 AM, Peter Haverty <haverty.peter at gene.com>
wrote:

Hi all,

I believe there is a strong need for an object that organizes a
collection
of rectangular data (matrices, etc.) with metadata on the rows and
columns.  Can SummarizedExperiment inherit from something simpler that
has
a DataFrame as rowData?  (I believe GenomicRanges should inherit from
DataTable, rather than Vector, and subset as x[i,j], but maybe that's
getting a bit off topic.)  I often see people stuffing arbitrary data
into
an ExpressionSet and calling one of the assays "exprs" as a
work-around.

Regards,

Pete

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