Instructions on how to use / save / read TileDBArrays in a SummarizedExperiment

[tomsing1]

So great to see the TileDBArray backend join the Bioconductor family 👍 .

A quick question: are you planning to create helper functions to save / read SummarizedExperiments with TileDBArray backends? Analogous to what Herve Pages has provided in the HDF5Array package here for instance?

Or perhaps there already are examples of how to persist TileDBArray-backed SummarizedExperiments that I could learn from?

[LTLA]

I wasn't planning to. I suppose it would be possible to fit in the multiple assays as separate TileDB attributes, and the metadata can probably be serialized for storage in the TileDB metadata, but I don't have a clear idea of how to deal with the rowData or colData. I suppose I could serialize them as well and put them into the metadata, but there ought to be a better approach that gives us slicing capabilities.

[PeteHaitch]

I interpreted the question differently. The HDF5Array functions only save the assay data to HDF5, the rowData, colData, etc. are serialised as .rds. Is that what you're asking for @tomsing1 ?

[tomsing1]

Thanks a lot for the quick responses! Yes, I was thinking along the lines of what the HDF5Array function does, e.g. store the rowData and colData in a different form (rds) but taking care of saving / loading them - like @PeteHaitch surmised.

Of course, if @LTLA has an even smarter idea to keep everything inside tiledb, that would be more than welcome, too.

[eddelbuettel]

(Just chiming in to say that we're all ears and happy to help. We can do some R-specific things in the tiledb R package for metadata serialization, we can (and very likely will "soon") do something generic at the TileDB library level (as we need similar features in other projects). It is all relatively new stuff, and I am currently focussed on gettting a TileDB Cloud R package up and running.)