It's probably good keeping coercion and construction distinct, although we have violated that recently with GRanges(). It now attempts to coerce its first argument to a GRanges. Don't want to derail the discussion, but it's another data point.
Michael On Mon, Sep 11, 2017 at 9:26 AM, Levi Waldron <lwaldron.resea...@gmail.com> wrote: > On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger < > ludwig.geistlin...@bio.ifi.lmu.de> wrote: > >> I guess we discussed this with Davide Risso @Bioc2017 in the >> MultiAssayExperiment workshop. >> >> > SummarizedExperiment(mouseData) >> >> puts the eSet (rather counterintuitively) into `assays` of >> `SummarizedExperiment`, it does not really coerce it to >> SummarizedExperiment, eg. `fData` and `pData` are not accordingly >> transferred to colData and rowData. >> > > Right, I had forgotten about that - this isn't a coercion but a > construction, which should be obvious from the use of a constructor > function. This behavior is intuitive if you remember that > SummarizedExperiment(assays, ...) is a constructor that accepts as assays > any object or list of objects supporting square bracket matrix-like > subsetting. Sorry for my brain hiccup there. > > >> While I can understand that this is by design of `SummarizedExperiment`, I >> really wonder whether there are use cases where somebody would like to put >> an `ExpressionSet` in `assays` of `SummarizedExperiment`, and not rather >> would like to coerce it that way. >> >> Furthermore, if you would indeed like to have several `ExpressionSet`s in >> a `SummarizedExperiment`, haven't you already arrived at a scenario where >> use of `MultiAssayExperiment` is indicated? >> > > I think the behavior of the constructor SummarizedExperiment() here is > correct and expected, the issue here is that we're actually looking for > coercion methods. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
