Subset HDF5AnnData?

[SNOL2]

Hi, is it possible to subset HDF5AnnData? I tried adata[adata$obs['label']=='int_label',] and encounterd the error "object of type 'environment' is not subsettable".
Thanks in advance!

[lazappi]

Subsetting a HDF5AnnData would be difficult as it is directly linked to a file that we would need to (temporarily) modify. I would need to check if it's possible to do that in Python but I suspect not. If you want to subset your data you will need to convert it (or at least the part you want) into an in-memory format. In fact, HDF5AnnData isn't really designed for users to interact with directly but that's another conversation.

There should probably be a nicer error message when people try to subset though as I can see people trying to do that.

[SNOL2]

Fine. Thanks for your answer!

[rcannood]

@lazappi We could implement an AnnDataView class, so that we can subset AnnData objects. Wdyt?

[lazappi]

I'm not sure that helps for the file-backed interfaces. I would probably check what Python let's you do and try to replicate that.

[Artur-man]

Probably related to #128 ? DelayedArray already has built-in support for lazy subsetting. If anndataR would go to BioC, probably it is better to cover a full DelayedArray support.