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/mvlmm.h | 94 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 94 insertions(+)
create mode 100644 src/mvlmm.h
(limited to 'src/mvlmm.h')
diff --git a/src/mvlmm.h b/src/mvlmm.h
new file mode 100644
index 0000000..129879c
--- /dev/null
+++ b/src/mvlmm.h
@@ -0,0 +1,94 @@
+/*
+ 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 __MVLMM_H__
+#define __MVLMM_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 MVLMM {
+
+public:
+ // IO related parameters
+ int a_mode; //analysis mode, 1/2/3/4 for Frequentist tests
+ size_t d_pace; //display pace
+
+ string file_bfile;
+ string file_geno;
+ string file_out;
+ string path_out;
+
+ // MVLMM related parameters
+ double l_min;
+ double l_max;
+ size_t n_region;
+ double logl_remle_H0, logl_mle_H0;
+ vector Vg_remle_null, Ve_remle_null, Vg_mle_null, Ve_mle_null;
+ vector VVg_remle_null, VVe_remle_null, VVg_mle_null, VVe_mle_null;
+ vector beta_remle_null, se_beta_remle_null, beta_mle_null, se_beta_mle_null;
+ double p_nr;
+ size_t em_iter, nr_iter;
+ double em_prec, nr_prec;
+ size_t crt;
+
+ // Summary statistics
+ size_t ni_total, ni_test; //number of individuals
+ size_t ns_total, ns_test; //number of snps
+ size_t n_cvt;
+ size_t n_ph;
+ double time_UtX; //time spent on optimization iterations
+ double time_opt; //time spent on optimization iterations
+
+ vector indicator_idv; //indicator for individuals (phenotypes), 0 missing, 1 available for analysis
+ vector indicator_snp; //sequence indicator for SNPs: 0 ignored because of (a) maf, (b) miss, (c) non-poly; 1 available for analysis
+
+ vector snpInfo; //record SNP information
+
+ // Not included in PARAM
+ vector sumStat; //Output SNPSummary Data
+
+ // Main functions
+ void CopyFromParam (PARAM &cPar);
+ void CopyToParam (PARAM &cPar);
+ void AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
+ void AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
+ void WriteFiles ();
+
+};
+
+void CalcMvLmmVgVeBeta (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY, const size_t em_iter, const size_t nr_iter, const double em_prec, const double nr_prec, const double l_min, const double l_max, const size_t n_region, gsl_matrix *V_g, gsl_matrix *V_e, gsl_matrix *B, gsl_matrix *se_B);
+
+#endif
+
+
--
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