def test_ssrge_cnv(self):
"""test ssrge procedure with cnv matrix"""
from garmire_SSrGE.examples import create_example_matrix_v3
from garmire_SSrGE.ssrge import SSrGE
X, Y, C, W = create_example_matrix_v3()
ssrge = SSrGE(alpha=0.01)
ssrge.fit(X, Y, C)
self.assertTrue(ssrge.eeSNV_weight)
Xr = ssrge.transform(X)
self.assertTrue(Xr.sum())
self.assertTrue(Xr.shape[0] == X.shape[0])
self.assertTrue(Xr.shape[1] < X.shape[1])
snv_ranked = ssrge.rank_eeSNVs()
self.assertTrue(snv_ranked)
score = ssrge.score(X, Y)
self.assertTrue(score[0] < score[1])
def test_ssrge_rank_gene(self):
"""test ssrge and rank genes and snvs"""
from garmire_SSrGE.examples import create_example_matrix_v2
from garmire_SSrGE.ssrge import SSrGE
X, Y, gene_id_list, snv_id_list = create_example_matrix_v2()
ssrge = SSrGE(snv_id_list=snv_id_list,
gene_id_list=gene_id_list,
nb_ranked_features=2,
alpha=0.01)
ssrge.fit(X, Y)
self.assertTrue(ssrge.eeSNV_weight)
Xr = ssrge.transform(X)
self.assertTrue(Xr.sum())
self.assertTrue(Xr.shape[0] == X.shape[0])
self.assertTrue(Xr.shape[1] < X.shape[1])
snv_ranked = ssrge.rank_eeSNVs()
self.assertTrue(snv_ranked)
self.assertTrue(len(ssrge.retained_snvs) == ssrge.nb_ranked_features)
self.assertTrue(len(ssrge.retained_genes) == ssrge.nb_ranked_features)
score = ssrge.score(X, Y)
self.assertTrue(score[0] < score[1])
subgroup = ssrge.rank_features_for_a_subgroup(range(10))
self.assertTrue(len(subgroup.gene_expr_distrib[gene_id_list[0]]) == 10)
self.assertTrue(subgroup.snv_weights_distrib)
self.assertTrue(subgroup.exp_snv_distrib_comp)
def test_ssrge_elasticnet(self):
"""test ssrge procedure with elasticnet model"""
from garmire_SSrGE.examples import create_example_matrix_v1
from garmire_SSrGE.ssrge import SSrGE
X, Y, W = create_example_matrix_v1()
ssrge = SSrGE(alpha=0.01, model='ElasticNet')
ssrge.fit(X, Y)
self.assertTrue(ssrge.eeSNV_weight)
Xr = ssrge.transform(X)
self.assertTrue(Xr.sum())
self.assertTrue(Xr.shape[0] == X.shape[0])
self.assertTrue(Xr.shape[1] <= X.shape[1])
snv_ranked = ssrge.rank_eeSNVs()
self.assertTrue(snv_ranked)
score = ssrge.score(X, Y)
self.assertTrue(score[0] < score[1])