From 7762722f264adc402ea3b0f21923b18f072253ba Mon Sep 17 00:00:00 2001
From: xiangzhou
Date: Mon, 22 Sep 2014 11:06:02 -0400
Subject: version 0.95alpha
---
src/vc.h | 82 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 82 insertions(+)
create mode 100644 src/vc.h
(limited to 'src/vc.h')
diff --git a/src/vc.h b/src/vc.h
new file mode 100644
index 0000000..f34d72e
--- /dev/null
+++ b/src/vc.h
@@ -0,0 +1,82 @@
+/*
+ Genome-wide Efficient Mixed Model Association (GEMMA)
+ Copyright (C) 2011 Xiang Zhou
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
+*/
+
+#ifndef __VC_H__
+#define __VC_H__
+
+#include "gsl/gsl_vector.h"
+#include "gsl/gsl_matrix.h"
+
+
+#ifdef FORCE_FLOAT
+#include "param_float.h"
+#include "io_float.h"
+#else
+#include "param.h"
+#include "io.h"
+#endif
+
+using namespace std;
+
+
+
+class VC_PARAM
+{
+
+public:
+ const gsl_matrix *K;
+ const gsl_matrix *W;
+ const gsl_vector *y;
+ gsl_matrix *P;
+ gsl_vector *Py;
+ gsl_matrix *KPy_mat;
+ gsl_matrix *PKPy_mat;
+ gsl_matrix *Hessian;
+};
+
+
+
+
+class VC {
+
+public:
+ // IO related parameters
+ string file_out;
+ string path_out;
+
+ vector v_sigma2;
+ vector v_se_sigma2;
+ vector v_pve;
+ vector v_se_pve;
+ vector v_traceG;
+ vector v_beta;
+ vector v_se_beta;
+
+ double time_UtX;
+ double time_opt;
+
+ // Main functions
+ void CopyFromParam (PARAM &cPar);
+ void CopyToParam (PARAM &cPar);
+ void CalcVChe (const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
+ void CalcVCreml (const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
+};
+
+#endif
+
+
--
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