decoupler.get_contrast
- decoupler.get_contrast(adata, group_col, condition_col, condition, reference, method='t-test')
Computes simple contrast between two conditions from pseudo-bulk profiles. After genertaing pseudo-bulk profiles with dc.get_pseudobulk, computes Differential Expression Analysis using scanpy’s rank_genes_groups function between two conditions.
- Parameters:
- adataAnnData
Input pseudo-bulk AnnData object.
- group_colstr
Column of obs where to extract the groups names.
- condition_colstr
Column of obs where to extract the condition names.
- conditionstr
Name of the condition to test inside condition_col.
- referencestr
Name of the reference to use inside condition_col.
- methodstr
Method to use for scanpy’s rank_genes_groups function.
- Returns:
- Returns logfoldchanges and p-values per gene.