updated the code to allow for non-chromsomal treatment.

negar7918 · Sep 28, 2022 · 3814f0d · 3814f0d
1 parent cda9b13
commit 3814f0d
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/CopyMix_Gaussian/inference.py b/CopyMix_Gaussian/inference.py
@@ -589,7 +589,8 @@ def vi(locs, prior, init, y, max_iter=15, tol=.000000001):
 
         for k in range(K):
             # handle chromosomal loci
-            p_prev.weight_vertex[k] = correct_for_chrom(p_prev.weight_vertex[k], locs)
+            if locs is not None:
+                p_prev.weight_vertex[k] = correct_for_chrom(p_prev.weight_vertex[k], locs)
             graph = C(M, p_prev.weight_initial[k], p_prev.weight_edge[k], p_prev.weight_vertex[k])
             # Update 3
             clusters.insert(k, graph)

diff --git a/CopyMix_Gaussian/initialization.py b/CopyMix_Gaussian/initialization.py
@@ -190,7 +190,7 @@ def generate_initializations(id, data, num_of_states, total_num_of_clusters):
             inits[index].add_init(delta, theta, tau, alpha_gam, beta_gam, lam, pi,
                                   weight_initial, weight_edge, weight_vertex)
             new_delta, new_theta, new_tau, new_alpha_gam, new_beta_gam, new_lam, new_pi, weight_initial, new_weight_edge, \
-            new_weight_vertex, trans = vi(prior, init, data)
+            new_weight_vertex, trans = vi(None, prior, init, data)
             inits[index].add_new(trans, new_delta, new_theta, new_tau, new_alpha_gam, new_beta_gam, new_lam, new_pi, weight_initial, new_weight_edge, \
             new_weight_vertex, vi.likelihood, "random_random"+str(i), k)
 
@@ -203,7 +203,7 @@ def generate_initializations(id, data, num_of_states, total_num_of_clusters):
             inits[index].add_init(delta, theta, tau, alpha_gam, beta_gam, lam, pi,
                                  weight_initial, weight_edge, weight_vertex)
             new_delta, new_theta, new_tau, new_alpha_gam, new_beta_gam, new_lam, new_pi, weight_initial, new_weight_edge, \
-            new_weight_vertex, trans = vi(prior, init, data)
+            new_weight_vertex, trans = vi(None, prior, init, data)
             inits[index].add_new(trans, new_delta, new_theta, new_tau, new_alpha_gam, new_beta_gam, new_lam, new_pi,
                                  weight_initial, new_weight_edge, new_weight_vertex, vi.likelihood, "random" + str(i), k)