smftools.preprocessing.calculate_coverage

smftools.preprocessing.calculate_coverage#

smftools.preprocessing.calculate_coverage(adata, ref_column='Reference_strand', position_nan_threshold=0.01, smf_modality='deaminase', target_layer='binarized_methylation', uns_flag='calculate_coverage_performed', force_redo=False)#

Append position-level coverage metadata per reference category.

Parameters:

  • adata (AnnData) -- AnnData object.

  • ref_column (str (default: 'Reference_strand')) -- Obs column used to define reference/strand categories.

  • position_nan_threshold (float (default: 0.01)) -- Minimum fraction of coverage to mark a position as valid.

  • smf_modality (str (default: 'deaminase')) -- SMF modality. Use adata.X for conversion/deaminase or target_layer for direct.

  • target_layer (str (default: 'binarized_methylation')) -- Layer used for direct SMF coverage calculations.

  • uns_flag (str (default: 'calculate_coverage_performed')) -- Flag in adata.uns indicating prior completion.

  • force_redo (bool (default: False)) -- Whether to rerun even if uns_flag is set.

Return type:

None