smftools.preprocessing.append_binary_layer_by_base_context

smftools.preprocessing.append_binary_layer_by_base_context#

smftools.preprocessing.append_binary_layer_by_base_context(adata, reference_column, smf_modality='conversion', verbose=True, uns_flag='append_binary_layer_by_base_context_performed', bypass=False, force_redo=False, from_valid_sites_only=False, valid_site_col_suffix='_valid_coverage')#

Build per-reference masked layers for base-context sites.

Parameters:

  • adata (AnnData) -- AnnData object to annotate.

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

  • smf_modality (str (default: 'conversion')) -- SMF modality identifier.

  • verbose (bool (default: True)) -- Whether to log layer summary information.

  • uns_flag (str (default: 'append_binary_layer_by_base_context_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.

  • from_valid_sites_only (bool (default: False)) -- Whether to use valid-coverage site masks only.

  • valid_site_col_suffix (str (default: '_valid_coverage')) -- Suffix for valid-coverage site columns.

Returns:

AnnData object with new masked layers.

Return type:

anndata.AnnData