decoupler.filter_by_prop

decoupler.filter_by_prop(adata, min_prop=0.2, min_smpls=2)

Determine which genes are expressed in a sufficient proportion of cells across samples.

This function selects genes that are sufficiently expressed across cells in each sample and that this condition is met across a minimum number of samples.

Parameters:

adataAnnData

AnnData obtained after running decoupler.get_pseudobulk. It requires .layer['psbulk_props'].

min_propfloat

Minimum proportion of cells that express a gene in a sample.

min_smplsint

Minimum number of samples with bigger or equal proportion of cells with expression than min_prop.

Returns:

genesndarray

List of genes to be kept.