spapros.ut.get_expression_quantile

spapros.ut.get_expression_quantile(adata, q=0.9, normalise=False, log1p=False, zeros_to_nan=False)

Compute each genes q’th quantile on normalised (and log1p) data.

Parameters:

• adata (AnnData) – AnnData object. If normalise is True we expect raw counts in adata.X and size factors in adata.obs['size_factors'].

• q (float) – Value between 0 = q = 1, the quantile to compute.

• normalise (bool) – Normalise data with a.obs[‘size_factors’].

• log1p (bool) – log1p the data to get quantile values of log data. Not necessary if log1p was already applied on adata.X.

• zeros_to_nan (bool) – Don’t include zeros into quantile calculation.

Return type:

None

Returns.

Adds column adata.var[f'quantile_{q}'] or adata.var[f'quantile_{} expr > 0']: