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. Best, Kasper On Tue, Jul 12, 2016 at 4:24 PM, Hervé Pagès <hpa...@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 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
