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tanaylab / metacells

Metacells - Single-cell RNA Sequencing Analysis
MIT License
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metacells2 'unknown mask data: lateral_gene' #70

Closed angelica-varesi closed 2 months ago

angelica-varesi commented 2 months ago

Hi, I am getting this error:

File "../python3.10/site-packages/metacells/tools/mask.py", line 87, in combine_masks raise KeyError(f"unknown mask data: {mask_name}") KeyError: 'unknown mask data: lateral_gene'

when I try to run this code to obtain Metacells mc.pl.divide_and_conquer_pipeline(raw, random_seed=123456, target_metacell_umis= 80000)

As row I input the counts RNA data in h5ad file.

I don't know how to solve the issue.

Thanks a lot for the help!!!!

orenbenkiki commented 2 months ago

You haven't set a lateral_gene mask. This is a mask of genes which shouldn't be considered when grouping cells to metacells (for example, cell-cycle, stress, etc.).

angelica-varesi commented 2 months ago

Thanks! However, I would like to set it as NULL since I don't want to have any gene excluded. Could you please send me the code for that? Thanks a lot!!!!

orenbenkiki commented 2 months ago

Just set it to an all-zero mask (np.zeros(n_genes, bool)). Of course it is likely that once you start computing metacells you'll discover that you actually want to mark some genes as literal and re-compute... but that depends on your data set.

angelica-varesi commented 2 months ago

Thanks a lot! Angelica