get the PSI for every alternative splicing event in every cell

[Laura-1997]

I want to know, can I get the PSI for every alternative splicing event in every cell ? Because I wanted to explore the correlation between splicing factors (SF) and splicing events through the expression levels of splicing factors in each cell and the PSI of splicing events in each cell.
How can I get the PSI for every alternative splicing event in every cell ? from which destination file ?
Thanks for your help.

[huangyh09]

Hi Laura,

Yes, you can obtain the PSI matrix for each event in each cell. The output .h5ad file stores an AnnData object, which contains the PSI matrix by adata.layers['Psi'], and its 95% confidence interval, adata.layers['Psi_95CI'], if you want to filter low confident quantifications.

Also, which mode are you using? It seems the aggregated imputation fits your case:
https://brie.readthedocs.io/en/latest/brie_quant.html#mode-2-aggregated-imputation

Yuanhua