[Bioc-devel] on the subject of combine, cbind and rbind

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Wed Jul 13 01:57:44 CEST 2016

Well, combine() has been extremely useful in my work and I would love to
have a version for SummarizedExperiment's.  I do appreciate that it might
not be the job of cbind.

merge did the work for me for DataFrame's.


On Tue, Jul 12, 2016 at 4:24 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Kasper,
> On 07/12/2016 09:31 AM, Kasper Daniel Hansen wrote:
>> combine() is the old style way of combining ExpressionSets and friends and
>> is pretty powerful, for example dealing with pData objects with different
>> columns (which is the case for almost all data).
>> It seems to me that cbind() on SummarizedExperiments is much less
>> powerful.  Specifically rbind() on DataFrame's (for colData) requires that
>> the two DataFrame's have the same columns.  I think this should be
>> addressed.
> A 1st little step that would maybe help would be to have rbind() on
> DataFrame objects work when the columns are the same but not in the
> same order. This is something that works with ordinary data frames.
> That being said, we might want to do more e.g. have cbind() on
> SummarizedExperiment objects work when the colData don't have the
> same columns.
> And I guess that would be pretty much it for the improvements to
> cbind,SummarizedExperiment. It needs to stick to the cbind semantic
> i.e. it should not try to merge assay columns and should preserve the
> nb of rows. As Michael pointed out, that kind of feature (i.e. merging
> assay columns and/or rows) would belong to something like a merge() or
> maybe a combine().
> H.
> It is not clear to me that rbind() doesn't do the right thing,
>> but in that case perhaps we do need combine() for SummarizedExperiment's
>> and DataFrame's
>> Or perhaps Im doing it wrong.
>> Best,
>> Kasper
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> --
> Hervé Pagès
> 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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