came.utils.preprocess.normalize_default

came.utils.preprocess.normalize_default(adata: AnnData, target_sum=None, copy: bool = False, log_only: bool = False, force_return: bool = False)

Normalizing datasets with default settings (total-counts normalization followed by log(x+1) transform).

Parameters:

  • adata – AnnData object

  • target_sum – scale factor of total-count normalization

  • copy – whether to copy the dataset

  • log_only – whether to skip the “total-counts normalization” and only perform log(x+1) transform

  • force_return – whether to return the data, even if changes are made for the original object

Return type:

AnnData or None