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

Hervé Pagès hpages at fredhutch.org
Tue Jul 12 22:24:24 CEST 2016

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().


> 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
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

More information about the Bioc-devel mailing list