omicverse.micro.rarefy

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omicverse.micro.rarefy#

omicverse.micro.rarefy(adata, depth=None, seed=0, drop_shallow=True, save_original=True, copy=False)[source]#

Rarefy counts to a common depth.

The rarefied matrix overwrites adata.X; the original counts are retained in adata.layers['counts_raw'] when save_original=True.

Parameters:

  • adata (AnnData) – Samples × features AnnData with int counts.

  • depth (Optional[int] (default: None)) – Target depth. If None, uses the minimum sample library size.

  • seed (int (default: 0)) – Random seed for reproducibility.

  • drop_shallow (bool (default: True)) – If True, samples with library size < depth are DROPPED. If False, their original counts are kept (no subsampling possible below depth).

  • save_original (bool (default: True)) – If True, a copy of the pre-rarefaction X is saved to adata.layers['counts_raw'].

  • copy (bool (default: False)) – Return a copy instead of modifying in place.

Return type:

AnnData

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