[Bioc-devel] Changes to the SummarizedExperiment Class

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.

[Bioc-devel] Changes to the SummarizedExperiment Class

Thread (16 messages)