[Bioc-devel] Plans for multi-feature SingleCellExperiment?

[Michael Lawrence]

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.honeypot using 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
>
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