From 17deca2d54827a00df3ea4d98df700fc2b8ed777 Mon Sep 17 00:00:00 2001
From: xiangzhou
Date: Sat, 20 Sep 2014 10:17:34 -0400
Subject: initial upload, version 0.95alpha
---
lmm.h | 110 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 110 insertions(+)
create mode 100644 lmm.h
(limited to 'lmm.h')
diff --git a/lmm.h b/lmm.h
new file mode 100644
index 0000000..d65b785
--- /dev/null
+++ b/lmm.h
@@ -0,0 +1,110 @@
+/*
+ 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 __LMM_H__
+#define __LMM_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 FUNC_PARAM
+{
+
+public:
+ bool calc_null;
+ size_t ni_test;
+ size_t n_cvt;
+ const gsl_vector *eval;
+ const gsl_matrix *Uab;
+ const gsl_vector *ab;
+ size_t e_mode;
+};
+
+
+
+
+class LMM {
+
+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 file_gene;
+
+ // LMM related parameters
+ double l_min;
+ double l_max;
+ size_t n_region;
+ double l_mle_null;
+ double logl_mle_H0;
+
+ // Summary statistics
+ size_t ni_total, ni_test; //number of individuals
+ size_t ns_total, ns_test; //number of snps
+ size_t ng_total, ng_test; //number of genes
+ size_t n_cvt;
+ 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 AnalyzeGene (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Utx, const gsl_matrix *W, const gsl_vector *x);
+ void AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y);
+ void AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y);
+ void WriteFiles ();
+
+ void CalcRLWald (const double &lambda, const FUNC_PARAM ¶ms, double &beta, double &se, double &p_wald);
+ void CalcRLScore (const double &l, const FUNC_PARAM ¶ms, double &beta, double &se, double &p_score);
+};
+
+void MatrixCalcLR (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, const double l_min, const double l_max, const size_t n_region, vector > &pos_loglr);
+void CalcLambda (const char func_name, FUNC_PARAM ¶ms, const double l_min, const double l_max, const size_t n_region, double &lambda, double &logf);
+void CalcLambda (const char func_name, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const double l_min, const double l_max, const size_t n_region, double &lambda, double &logl_H0);
+void CalcPve (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const double lambda, const double trace_G, double &pve, double &pve_se);
+void CalcLmmVgVeBeta (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const double lambda, double &vg, double &ve, gsl_vector *beta, gsl_vector *se_beta);
+
+#endif
+
+
--
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