[Bioc-devel] Changes to the SummarizedExperiment Class
Hi Mike, Our error - we didn't bump GenomicRanges when rowRanges was added. Hopefully 1.19.43 will propagate today and things will be sorted out. Val
On 03/06/2015 07:40 AM, Michael Love wrote:
hi all, just a practical issue: I have GenomicRanges version 1.19.42 on my computer which does not have rowRanges defined, although the 1.19.42 version on the Bioc website does have rowRanges in the man page: http://master.bioconductor.org/packages/3.1/bioc/html/GenomicRanges.html So I pass check locally but not in the devel branch on Bioc servers.
library(GenomicRanges) rowRanges
Error: object 'rowRanges' not found
sessionInfo()
R Under development (unstable) (2014-12-08 r67137)
Platform: x86_64-apple-darwin12.5.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices datasets utils
methods base
other attached packages:
[1] GenomicRanges_1.19.42 GenomeInfoDb_1.3.13 IRanges_2.1.41
S4Vectors_0.5.21
[5] BiocGenerics_0.13.6 RUnit_0.4.28 devtools_1.7.0 knitr_1.9
[9] BiocInstaller_1.17.5
On Wed, Mar 4, 2015 at 3:03 PM, Martin Morgan <mtmorgan at fredhutch.org> wrote:
On 03/04/2015 10:03 AM, Peter Haverty wrote:
Michael has a good point. The complexity of the BioC universe of classes hurts our ability to attract new users. More classes would be a minus there ... but a small set of common, explicit APIs would simplify things. Rectangular things implement the matrix Interface. :-) Deprecating old stuff, like eSet, might help more than it hurts, on the simplicity front. P.S. apropos of understanding this universe of classes, I *love* the methods(class=x) thing Vincent mentioned.
The current version, under R-devel, is at
devtools::source_gist("https://gist.github.com/mtmorgan/9f98871adb9f0c1891a4")
> methods(class="SummarizedExperiment")
[1] [ [[ [[<- [<-
[5] $ $<- assay assay<-
[9] assayNames assayNames<- assays assays<-
[13] cbind coerce colData colData<-
[17] compare Compare countOverlaps coverage
[21] dim dimnames dimnames<- disjointBins
[25] distance distanceToNearest duplicated elementMetadata
[29] elementMetadata<- end end<- exptData
[33] exptData<- extractROWS findOverlaps flank
[37] follow granges isDisjoint mcols
[41] mcols<- narrow nearest order
[45] overlapsAny precede ranges ranges<-
[49] rank rbind replaceROWS resize
[53] restrict rowData rowData<- seqinfo
[57] seqinfo<- seqnames shift show
[61] sort split start start<-
[65] strand strand<- subset subsetByOverlaps
[69] updateObject values values<- width
[73] width<-
see ?"methods" for accessing help and source code
and
head(attr(methods(class="SummarizedExperiment"), "info"))
generic visible
[,SummarizedExperiment,ANY-method [ TRUE
[[,SummarizedExperiment,ANY,missing-method [[ TRUE
[[<-,SummarizedExperiment,ANY,missing-method [[<- TRUE
[<-,SummarizedExperiment,ANY,ANY,SummarizedExperiment-method [<- TRUE
$,SummarizedExperiment-method $ TRUE
$<-,SummarizedExperiment-method $<- TRUE
isS4 from
[,SummarizedExperiment,ANY-method TRUE GenomicRanges
[[,SummarizedExperiment,ANY,missing-method TRUE GenomicRanges
[[<-,SummarizedExperiment,ANY,missing-method TRUE GenomicRanges
[<-,SummarizedExperiment,ANY,ANY,SummarizedExperiment-method TRUE GenomicRanges
$,SummarizedExperiment-method TRUE GenomicRanges
$<-,SummarizedExperiment-method TRUE GenomicRanges
Martin
Pete
____________________
Peter M. Haverty, Ph.D.
Genentech, Inc.
phaverty at gene.com
On Wed, Mar 4, 2015 at 9:38 AM, Michael Lawrence <lawrence.michael at gene.com>
wrote:
I think we need to make sure that there are enough benefits of something
like GRangesFrame before we introduce yet another complicated and
overlapping data structure into the framework. Prior to summarization, the
ranges seem primary, after summarization, it may often make sense for them
to be secondary. But I'm just not sure what we gain from a new data
structure.
On Wed, Mar 4, 2015 at 12:28 AM, Herv? Pag?s <hpages at fredhutch.org> wrote:
GRangesFrame is an interesting idea and I gave it some thoughts.
There is this nice symmetry between GRanges and GRangesFrame:
- GRanges = a naked GRanges + a DataFrame accessible via mcols()
- GRangesFrame = a DataFrame + a naked GRanges accessible via
some accessor (e.g. rowRanges())
So GRanges and GRangesFrame are equivalent in terms of what they
can hold, but different in terms of API: the former has the ranges
API as primary API and the DataFrame API on its mcols() component,
and the latter has the DataFrame API as primary API and the ranges
API on its rowRanges() component. Nice switch!
What does this API switch bring us? A GRangesFrame object is now
an object that fully behaves like a DataFrame and people can also
perform range-based operations on its rowRanges() component.
Here is what I'm afraid is going to happen: people will also want
to be able to perform range-based operations *directly* on
these objects, i.e. without having to call rowRanges() first.
So for example when they do subsetByOverlaps(), subsetting
happens vertically. Also the Hits object returned by findOverlaps()
would contain row indices. Problem with this is that these objects
now start to suffer from the "dual personality syndrome". For
example, it's not clear anymore what their length should be.
Strictly speaking it should be their number of columns (that's
what the length of a DataFrame is), but the ranges API that
we're trying to put on them also makes them feel like vectors
along the vertical dimension so it also feels that their length
should be their number of rows. Same thing with 1D subsetting.
Why does it subset the columns and not the rows? Most people
are now confused.
It's interesting to note that the same thing happens with GRanges
objects, but in the opposite direction: people wish they could
do DataFrame operations directly on them without calling mcols()
first. But in order to preserve the good health of GRanges objects,
we've not done that (except for $, a shortcut for mcols(x)$,
the pressure was just too strong).
H.
On 03/03/2015 04:35 PM, Michael Lawrence wrote:
Should be possible for the annotations to be of any type, as long as they
satisfy a simple contract of NROW() and 2D "[". Then, you could have a
DataFrame, GRanges, or whatever in there. But it would be nice to have a
special class for the container with range information. The contract for
the range annotation would be to have a granges() method.
I agree it would be nice if there was a way with the methods package to
easily assert such contracts. For example, one could define an interface
with a set of generics (and optionally the relevant position in the
generic
signature). Then, once all of the methods have been assigned for a
particular class, it is made to inherit from that contract class. There
are
lots of gotchas though. Not sure how useful it would be in practice.
On Tue, Mar 3, 2015 at 4:07 PM, Peter Haverty <haverty.peter at gene.com>
wrote:
There are some nice similarities in these new imaginary types. A
"GRangesFrame" is a list of dimensionally identical things (columns) and
some row meta-data (the GRanges). The SE-like object is similarly a
list
of dimensionally like things (matrices, RleDataFrames, BigMatrix
objects,
HDF5-backed things) with some row meta-data (a DataFrame or
GRangesFrame).
Elegant? Maybe they would actually be relatives in the class tree.
I wonder if this kind of thing would be easier if we had Java-style
Interfaces or duck-typing. The "x" slot of "y" holds something that
implements this set of methods ...
Oh, and kinda apropos, the genoset class will probably go away or become
an extension to this new SE-like thing. The extra stuff that comes
along
with genoset will still be available.
Pete
____________________
Peter M. Haverty, Ph.D.
Genentech, Inc.
phaverty at gene.com
On Tue, Mar 3, 2015 at 3:42 PM, Tim Triche, Jr. <tim.triche at gmail.com>
wrote:
This.
It would be damned near perfect as a return value for assays coming
out of
an object that held several such assays at several time points in a
population, where there are both assay-wise and covariate-wise "holes"
that
could nonetheless be usefully imputed across assays.
Statistics is the grammar of science.
Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
On Tue, Mar 3, 2015 at 3:25 PM, Peter Haverty <haverty.peter at gene.com>
wrote:
I still think GRanges should be a subclass of DataFrame,
which would make this easy, but I don't seem to be winning that
argument.
Just impossible. As Michael mentioned back in November, they have
conflicting APIs.
Maybe a new "GRangesFrame" that is a DataFrame and holds a GRanges
(without mcols) as an index?
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--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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