omicverse.micro.collapse_taxa

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omicverse.micro.collapse_taxa#

omicverse.micro.collapse_taxa(adata, rank='genus', unassigned_label='Unassigned')[source]#

Collapse ASVs to a taxonomic rank.

Returns a NEW AnnData where var_names are taxonomic labels at the chosen rank and counts are summed across ASVs sharing that label.

Parameters:

  • adata (AnnData)

  • rank (str (default: 'genus'))

  • unassigned_label (str (default: 'Unassigned'))

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