smftools.preprocessing.calculate_read_modification_stats

smftools.preprocessing.calculate_read_modification_stats(adata, reference_column, sample_names_col, mod_target_bases, uns_flag='calculate_read_modification_stats_performed', bypass=False, force_redo=False, valid_sites_only=False, valid_site_suffix='_valid_coverage', smf_modality='conversion')

Add methylation/deamination statistics for each read.

Parameters:

• adata (AnnData) -- AnnData object.

• reference_column (str) -- Obs column containing reference identifiers.

• sample_names_col (str) -- Obs column containing sample identifiers.

• mod_target_bases (list[str]) -- List of target base contexts (e.g., ["GpC", "CpG"]).

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

• bypass (bool (default: False)) -- Whether to skip processing.

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

• valid_sites_only (bool (default: False)) -- Whether to restrict to valid coverage sites.

• valid_site_suffix (str (default: '_valid_coverage')) -- Suffix used for valid-site matrices.

Return type:

None