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.

Returns:

adata : anndata.AnnData 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.