omicverse.pp.scrublet_simulate_doublets

omicverse.pp.scrublet_simulate_doublets(adata, *, layer=None, sim_doublet_ratio=2.0, synthetic_doublet_umi_subsampling=1.0, random_seed=0)[source]

Simulate synthetic doublets from random cell pairs.

Parameters:

  • adata (AnnData) – Input AnnData with observed cell transcriptomes.

  • layer (str, optional) – Layer key to use as input matrix. Uses adata.X when None.

  • sim_doublet_ratio (float, default=2.0) – Number of simulated doublets relative to observed cells.

  • synthetic_doublet_umi_subsampling (float, default=1.0) – UMI subsampling fraction used when creating synthetic doublets.

  • random_seed (int or RandomState, default=0) – Random state controlling pair sampling reproducibility.

Returns:

Synthetic-doublet AnnData containing simulated matrix and metadata.

Return type:

AnnData