cospar.tl.clonal_fate_bias

cospar.tl.clonal_fate_bias(adata, selected_fate='', alternative='two-sided', multiple_hypothesis_correction=False)

Compute clonal fate bias towards a cluster.

The clonal fate bias is -log(Q-value). We calculated a P-value that that a clone is enriched (or depleted) in a fate, using Fisher-Exact test (accounting for clone size). The P-value is then corrected to give a Q-value by Benjamini-Hochberg procedure. The alternative hypothesis options are: {‘two-sided’, ‘greater’, ‘less’}. The default is ‘two-sided’. With two-sided, we simply take less likely scenario either ‘greater’ and ‘less’ hypothesis.

Parameters

adata : AnnData object

selected_fate : str

The targeted fate cluster, from adata.obs[‘state_info’].

alternative : str, optional (default: ‘two-sided’)

Defines the alternative hypothesis. The following options are available (default is ‘two-sided’): ‘two-sided’; ‘less’: one-sided; ‘greater’: one-sided

Returns

result (pd.DataFrame)