decoupler.get_pseudobulk
- decoupler.get_pseudobulk(adata, sample_col, groups_col, obs=None, layer=None, min_prop=0.2, min_cells=10, min_counts=1000, min_smpls=2)
Generates an unormalized pseudo-bulk profile per sample and group.
Sums the counts of the cells belonging the the same sample and group. Genes that are not expressed in at least a proportion of cells (min_prop) and a number of samples (min_smpls) are ignored. This is done to remove noisy genes.
- Parameters:
- adataAnnData
Input AnnData object.
- sample_colstr
Column of obs where to extract the samples names.
- groups_colstr
Column of obs where to extract the groups names.
- obspd.DataFrame, None
If provided, meta-data dataframe.
- layerstr
If provided, which element of layers to use.
- min_propfloat
Minimum proportion of cells with non-zero values.
- min_cellsint
Minimum number of cells per sample.
- min_countsint
Minimum number of counts per sample.
- min_smplsint
Minimum number of samples per feature.
- Returns:
- Returns new AnnData object with unormalized pseudobulk profiles per sample
- and group.