Hi!

I am trying to extract the Probability of observation matrix (regions by cells) from a trained model. Is this automatically saved in the AnnData object?

Thank you

Hi!

I am trying to extract the Probability of observation matrix (regions by cells) from a trained model. Is this automatically saved in the AnnData object?

Thank you

Hi!

We donâ€™t generate or save it by default, but you can generate it using:

`model.get_accessibility_estimates(adata)`

.

Some notes on using it:

1 - do you want the estimated probability of *accessibility* or the probability of *observation*? This method by default gives the former (i.e after removing cell-specific and region-specific biases).

If you want the probability of *observation*, youâ€™ll want to re-introduce those biases by setting `normalize_cells=True, normalize_regions=True`

.

2 - the output can be quite large (since the matrix is dense). You can shrink the size by only generating the estimates for some cells / some regions (using the `indices`

and `region_indices`

arguments, respectively); alternatively, you can threshold the output so that estimates below some given threshold are replaced with 0s, and the output matrix is sparse.

Thank you for the detailed response! Very helpful