tomas.auxi.correctUMI

tomas.auxi.correctUMI(adata, groupby, method='upsampling', logUMIby=None)

Correct UMI to meet the estimated total-mRNA-ratio.

Parameters:

  • adata (AnnData) – The (annotated) UMI count matrix of shape n_obs × n_vars. Rows correspond to droplets and columns to genes.

  • groupby (str) – The key of the droplet categories stored in adata.obs.

  • logUMIby (str, optional) – The key of total UMIs in log2 stored in adata.obs. The default is None.

Returns:

adata_rc – The corrected UMI count matrix.

Return type:

TYPE