omicverse.metabol.normalize

omicverse.metabol.normalize(adata, *, method='pqn', reference='median', missing_threshold=0.5)

Normalize each sample (row) of adata.X to correct for dilution.

Parameters:

• method (Literal['pqn', 'tic', 'median', 'mstus'] (default: 'pqn')) – "pqn" (Dieterle 2006, recommended), "tic", "median", or "mstus".

• reference (Literal['median', 'mean'] (default: 'median')) – Only used by "pqn". The reference sample is the element-wise median (robust) or mean (noisier) of all samples. MetaboAnalyst uses median by default; we match.

• missing_threshold (float (default: 0.5)) – Only used by "mstus". Features missing in a higher fraction of samples are excluded from the denominator sum.

Return type:

AnnData