smftools.preprocessing.binarize_on_Youden

smftools.preprocessing.binarize_on_Youden#

smftools.preprocessing.binarize_on_Youden(adata, ref_column='Reference_strand', output_layer_name='binarized_methylation', mask_failed_positions=True)#

Binarize SMF values using thresholds from calculate_position_Youden.

Parameters:

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

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

  • output_layer_name (str (default: 'binarized_methylation')) -- Layer in which to store the binarized matrix.

  • mask_failed_positions (bool (default: True)) -- If True, positions that failed Youden QC are set to NaN; otherwise all positions are binarized.

Return type:

None