Is it possible to concatenate objects instead of using AnnDataSet?

[vitkl]

Hi again

Is it possible to concatenate AnnData objects for multiple samples instead of using AnnDataSet?

data = snap.AnnDataSet(adatas=h5ad_files, filename="colon.h5ads")

I need to add multiome RNA counts to the same object (as well as other varm/var/obsm/obs slots) and I am not sure how AnnDataSet works for this purpose.

[kaizhang]

SnapATAC2 doesn't support concatenating AnnData objects with different var_names (vertical stacking). You may be able to use anndata's function to achieve this: https://anndata.readthedocs.io/en/latest/generated/anndata.concat.html#anndata.concat

[vitkl]

So if I use anndata.concat on SnapATAC2 AnnData objects with identical var_names, I will get a new SnapATAC2 AnnData
object, that will work with various functions described in this tutorial https://kzhang.org/SnapATAC2/tutorials/pbmc.html? (eg add_tile_matrix call_peaks make_peak_matrix)

[kaizhang]

SnapATAC2 stores TN5 insertion counts in .obsm['insertion'] and uses that to call peaks, and compute cell by bin or cell by peak matrix. These functions don't care what you store in var_names. This is also true for other functions like tl.spectral. So in theory they should work.