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
Just to clarify further, .get_accessibility_estimates(adata)
by default
returns y_ij
and with .get_accessibility_estimates(adata, normalize_cells=True, normalize_regions=True)
you get y_ij * l_i * r_j
?
Can the adata
be different to the adata
used for training given that the object contains all the same columns/slots? I would like to compute accessibility estimates for cells not seen during traning.
Yes
Yes, we have an extensive validation procedure that will flag any inconsistencies in the new data.