decoupler.get_contrast
- decoupler.get_contrast(adata, group_col, condition_col, condition, reference=None, method='t-test')
Computes Differential Expression Analysis using scanpy’s rank_genes_groups function between two conditions from pseudo-bulk profiles.
- Parameters:
- adataAnnData
Input pseudo-bulk AnnData object.
- group_colstr, None
Column of obs where to extract the groups names, for example cell types. If None, do not group.
- condition_colstr
Column of obs where to extract the condition names, for example disease status.
- conditionstr
Name of the condition to test inside condition_col.
- referencestr
Name of the reference to use inside condition_col. If ‘rest’ or None, compare each group to the union of the rest of the group.
- methodstr
Method to use for scanpy’s rank_genes_groups function.
- Returns:
- logFCsDataFrame
Dataframe containing log-fold changes per gene.
- p_valsDataFrame
Dataframe containing p-values per gene.