From 7b5d6a4997ef37575f79295a2eb62f2354d0fccb Mon Sep 17 00:00:00 2001
From: hanna julienne <hanna.julienne@pasteur.fr>
Date: Fri, 2 Mar 2018 18:13:25 +0100
Subject: [PATCH] Impg model function
---
impute_jass/impute_jass/stat_models.py | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
create mode 100644 impute_jass/impute_jass/stat_models.py
diff --git a/impute_jass/impute_jass/stat_models.py b/impute_jass/impute_jass/stat_models.py
new file mode 100644
index 0000000..9937442
--- /dev/null
+++ b/impute_jass/impute_jass/stat_models.py
@@ -0,0 +1,22 @@
+"""
+function for SNP imputation
+
+"""
+import numpy
+
+def ImpG_model(Zt, Sig_t, Sig_i_t):
+ """
+ Argument:
+ Zt : (vector) the vector of known Z scores
+
+ """
+
+ np.fill_diagonal(Sig_t.values, 1.01)
+ Sig_t.fillna(0, inplace=True)
+
+ Sig_t_inv =np.linalg.inv(Sig_t)
+
+ Var = np.diag(Sig_t)[0] - np.einsum('ij,jk,ki->i', Sig_i_t, Sig_t_inv ,Sig_i_t.transpose())
+
+ mu = np.dot(Sig_i_t, np.dot(Sig_t_inv, Zfile.loc[index_known, 'Z']))
+ return((Var, mu))
--
GitLab