On branch conditional_independent

minor change
sejooning · Oct 4, 2013 · 1b61be4 · 1b61be4
1 parent f1d6682
commit 1b61be4
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Showing 3 changed files with 17 additions and 7 deletions.
diff --git a/pyloh/constants.py b/pyloh/constants.py
@@ -21,6 +21,7 @@
 BURN_IN = 10
 EPS = np.finfo(float).eps
 
+SIGMA = 0.01
 ERR = 0.01
 EMPIRI_BAF = 0.485
 EMPIRI_AAF = 1 - EMPIRI_BAF

diff --git a/pyloh/model/poisson_model.py b/pyloh/model/poisson_model.py
@@ -31,6 +31,7 @@ def preprocess(self):
         config_parameters['genotypes_tumor_num'] = get_genotypes_tumor_num(self.allele_number_max)
         config_parameters['alleletypes_tumor'] = get_alleletypes_tumor(self.allele_number_max)
         config_parameters['copynumber_tumor'] = get_copynumber_tumor(self.allele_number_max)
+        config_parameters['copynumber_tumor_num'] = get_copynumber_tumor_num(self.allele_number_max)
         config_parameters['MU_T'] = get_MU_T(self.allele_number_max)
 
         self.config_parameters = config_parameters

diff --git a/pyloh/model/utils.py b/pyloh/model/utils.py
@@ -88,16 +88,24 @@ def get_alleletypes_tumor(allele_number_max):
 
     return alleletypes_tumor
 
+#def get_copynumber_tumor(allele_number_max):
+#    copynumber_tumor = []
+#    
+#    for B_num in range(0, allele_number_max + 1):
+#        for A_num in range(0, allele_number_max + 1):
+#            c_T = A_num + B_num
+#                
+#            copynumber_tumor.append(c_T)
+#    
+#    return copynumber_tumor
+
 def get_copynumber_tumor(allele_number_max):
-    copynumber_tumor = []
 
-    for B_num in range(0, allele_number_max + 1):
-        for A_num in range(0, allele_number_max + 1):
-            c_T = A_num + B_num
-
-            copynumber_tumor.append(c_T)
+    return range(0, allele_number_max*2 + 1)
+
+def get_copynumber_tumor_num(allele_number_max):
 
-    return copynumber_tumor
+    return allele_number_max*2
 
 def get_MU_T(allele_number_max):
     empiri_BAF = constants.EMPIRI_BAF