scFates.tl.test_association_monocle3¶
- scFates.tl.test_association_monocle3(adata, qval_cut=0.0001, n_jobs=1, copy=False, **kwargs)¶
Determine a set of genes significantly associated with the trajectory.
the function graph_test monocle3 R package is called, using neighbor_graph = ‘principal_graph’ parameter. The statistic tells you whether cells at nearby positions on a trajectory will have similar (or dissimilar) expression levels for the gene being tested.
- Parameters
- adata :
AnnData Annotated data matrix.
- qval_cut :
float(default:0.0001) cutoff on the corrected p-values to consider a feature as significant.
- n_jobs :
bool(default:1) number of cpu processes used to perform the test.
- spline_df
dimension of the basis used to represent the smooth term.
- copy :
bool(default:False) Return a copy instead of writing to adata.
- adata :
- Returns
adata – if copy=True it returns or else add fields to adata: .var[‘status’]
The feature could be tested.
- .var[‘p_value’]
p-values from statistical test.
- .var[‘morans_test_statistic’]
Statistics of the Moran test
- .var[‘morans_I’]
Moran’s I is a measure of multi-directional and multi-dimensional spatial autocorrelation.
- .var[‘q_value’]
corrected values from multiple testing.
- ’.var[‘signi’]`
feature has q_value below cutoff.
- Return type