multi_dendrix.evaluate.matrix.matrix_permutation_test¶

multi_dendrix.evaluate.matrix.matrix_permutation_test(W_prime, permuted_matrices, t, k_min, k_max, alpha, delta, lmbda)[source]¶

Computes the statistical significance of a collection found by Multi-Dendrix using an empricial distribution of mutation data.

Parameters:

W_prime (int) – sum of the weights of an optimal collection of gene sets identified by Multi-Dendrix. This function compares this score to the optimal score on permuted mutation data.
permuted_matrices (list) – contains the mutation data tuples loaded by load_permuted_matrices().
t (int) – number of gene sets
k_min (int) – minimum gene set size.
k_max (int) – maximum gene set size.
alpha (float) – modifies the weight function W by changing the tradeoff between coverage and coverage overlap (default: 1.0).
delta (float) – number of delta allowed between any pair of gene sets (default: 0).
lmbda (int) – number of gene sets any gene can be a member of (default: 1).

Returns:

p-value (float) equal to the number of permuted matrices with greater W’, divided by the number of permuted matrices.