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 inadata.X
and size factors inadata.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}']
oradata.var[f'quantile_{} expr > 0']
: