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)