Hi Steve, Pretty sure MultiAssayExperiment, containing SingleCellExperiments, would fit the bill, but I'm not familiar with those data types.
Michael On Tue, Jan 22, 2019 at 2:18 PM Steve Lianoglou <mailinglist.honey...@gmail.com> wrote: > > Comrades, > > Sorry if I'm out of the loop and have missed anything obvious. > > I was curious what the plans are in the single-cell bioconductor-verse > to support single cell experiments that produce counts from different > feature-spaces, such as those produced by CITE-seq / REAP-seq, for > instance. > > In these types of experiments, I'm pretty sure we want the counts > generated from those "features" (oligo-conjugated Antibodies, for > instance) to be kept in a separate space than the mRNA counts. I think > we would most naturally want to put these in something like an > `assay()` matrix with a different (rowwise) dimmension than the gene > count matrix, but that can't work since all matrices in the assay() > list need to be of the same dimensions. > > Another option might be to just add them as rows to the assay > matrices, but keep some type of feature space meta-information akin to > what `isSpike()` currently does; > > or add a new slot to SingleCellExperiment to hold counts from > different feature spaces, perhaps?; > > Or rely on something like a MultiAssayExperiment? > > Or? > > Curious to learn which way you folks are leaning ... > > Thanks! > -steve > > ps - sorry if this email came through twice, it was somehow magically > sent from an email address I don't have access to anymore. > > -- > Steve Lianoglou > Denali Therapeutics > > _______________________________________________ > 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
