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theislab / scCODA

A Bayesian model for compositional single-cell data analysis
BSD 3-Clause "New" or "Revised" License
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Exporting Summary Results #80

Closed antonio-miranda closed 4 months ago

antonio-miranda commented 11 months ago

Hello,

I have run the tool on a dataset with over 50 cell types. I would like to export the individuals columns from the summary() output. I.e, I would like to get the log2 fold chances and the final parameter values, so that I can construct a table for custom plotting. Is there any way to do this?

Thanks in advance

johannesostner commented 11 months ago

Hi @antonio-miranda,

as stated in our advanced tutorial under "Extended model summary", you can access the intercepts part of the result as a DataFrame through result.intercept_df, and the effects DataFrame (with log2 fold changes, etc.) through result.effect_df.