decoupler.pp.filter_samples

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decoupler.pp.filter_samples#

decoupler.pp.filter_samples(adata, min_cells=10, min_counts=1000, inplace=True)#

Remove pseudobulked samples with insufficient number of cells and total counts.

Parameters:

  • adata (AnnData) – Annotated data matrix with observations (rows) and features (columns).

  • min_cells (int | float (default: 10)) – Minimum number of cells per sample.

  • min_counts (int | float (default: 1000)) – Minimum number of counts per sample.

  • inplace (bool (default: True)) – Whether to perform the operation in the same object.

Return type:

None | ndarray

Returns:

If inplace=False, array of samples to be kept.

Example

import decoupler as dc

adata = dc.ds.covid5k()
pdata = dc.pp.pseudobulk(adata, sample_col="individual", groups_col="celltype")
dc.pp.filter_samples(pdata, min_cells=10, min_counts=1000)
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