mira.tl.get_NITE_score_cells#
- mira.tl.get_NITE_score_cells(adata, counts_layer=None, median_nonzero_expression=None)#
Calculates the NITE score (Non-locally Influence Transcriptional Expression) for each cell. The NITE score quantifies how well changes in local chromatin accessibility explain changes in gene expression in that cell.
- Parameters
- adataanndata.AnnData
Adata of expression features per cell. This data must first be annotated with “LITE_logp” and “NITE_logp” using LITE and NITE RP models’ get_logp function.
- Returns
- adataanndata.AnnData
- .obs[“NITE_score”]np.ndarray[float] of shape (n_cells,)
Cell NITE score.
- Raises
- KeyErrorif adata is missing “LITE_logp” or “NITE_logp”
Examples
>>> rp_args = dict(expr_adata = atac_data, expr_adata = rna_data) >>> litemodel.predict(**rp_args) >>> nitemodel.predict(**rp_args) >>> mira.tl.get_NITE_score_cells(rna_data)