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-rw-r--r--src/lmm.h113
1 files changed, 67 insertions, 46 deletions
diff --git a/src/lmm.h b/src/lmm.h
index efbda4d..1e88cec 100644
--- a/src/lmm.h
+++ b/src/lmm.h
@@ -1,6 +1,6 @@
-/*
- Genome-wide Efficient Mixed Model Association (GEMMA)
- Copyright (C) 2011 Xiang Zhou
+/*
+ Genome-wide Efficient Mixed Model Association (GEMMA)
+ Copyright (C) 2011-2017, 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
@@ -13,7 +13,7 @@
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 <http://www.gnu.org/licenses/>.
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __LMM_H__
@@ -21,22 +21,12 @@
#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
-{
+class FUNC_PARAM {
public:
bool calc_null;
@@ -48,15 +38,12 @@ public:
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
+ // 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;
@@ -75,42 +62,76 @@ public:
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 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
+ double time_UtX; // Time spent on optimization iterations.
+ double time_opt; // Time spent on optimization iterations.
- vector<int> indicator_idv; //indicator for individuals (phenotypes), 0 missing, 1 available for analysis
- vector<int> indicator_snp; //sequence indicator for SNPs: 0 ignored because of (a) maf, (b) miss, (c) non-poly; 1 available for analysis
+ // Indicator for individuals (phenotypes): 0 missing, 1
+ // available for analysis.
+ vector<int> indicator_idv;
- vector<SNPINFO> snpInfo; //record SNP information
+ // Sequence indicator for SNPs: 0 ignored because of (a) maf,
+ // (b) miss, (c) non-poly; 1 available for analysis.
+ vector<int> indicator_snp;
- // Not included in PARAM
- vector<SUMSTAT> sumStat; //Output SNPSummary Data
+ vector<SNPINFO> snpInfo; // Record SNP information.
- // Main functions
+ // Not included in PARAM.
+ vector<SUMSTAT> 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);
- // WJA added
- void Analyzebgen (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 AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y, const gsl_vector *env);
- void AnalyzeBimbamGXE (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y, const gsl_vector *env);
+ 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);
+ // WJA added.
+ void Analyzebgen (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 AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval,
+ const gsl_matrix *UtW, const gsl_vector *Uty,
+ const gsl_matrix *W, const gsl_vector *y,
+ const gsl_vector *env);
+ void AnalyzeBimbamGXE (const gsl_matrix *U, const gsl_vector *eval,
+ const gsl_matrix *UtW, const gsl_vector *Uty,
+ const gsl_matrix *W, const gsl_vector *y,
+ const gsl_vector *env);
void WriteFiles ();
- void CalcRLWald (const double &lambda, const FUNC_PARAM &params, double &beta, double &se, double &p_wald);
- void CalcRLScore (const double &l, const FUNC_PARAM &params, double &beta, double &se, double &p_score);
+ void CalcRLWald (const double &lambda, const FUNC_PARAM &params,
+ double &beta, double &se, double &p_wald);
+ void CalcRLScore (const double &l, const FUNC_PARAM &params,
+ 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<pair<size_t, double> > &pos_loglr);
-void CalcLambda (const char func_name, FUNC_PARAM &params, 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);
+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<pair<size_t, double> > &pos_loglr);
+void CalcLambda (const char func_name, FUNC_PARAM &params,
+ 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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