pseudodynamics.de_test._association_test.AssociationTest

class pseudodynamics.de_test._association_test.AssociationTest(gam_fit, lineage_names)

Bases: object

Python implementation of tradeSeq associationTest

Parameters:

• gam_fit (dict) – The result of pdp.de_test.fitGAM

• lineage_names (list) – the names of lineages, lineage can be determined by tools like palantire or cellrank

Example

>>> gam_fit = de_test.run_fitGAM_parallel(expression_matrix, cell_time, genes, n_cores=10)
>>> test = de_test.AssociationTest(gam_fit, ['Ery'])
>>> result_lin_day = test.association_test(restrcited_pseudotime=pseudotime_range)

Methods table

association_test([global_test, lineages, ...])

Methods

AssociationTest.association_test(global_test=True, lineages=False, l2fc=0, contrast_type='start', n_points=None, restrcited_pseudotime=None, inverse='qr')

Return type:

DataFrame

Parameters:

• global_test (bool)

• lineages (bool)

• l2fc (float)

• contrast_type (str)

• n_points (int | None)

• restrcited_pseudotime (List | None)

• inverse (str)