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Diffstat (limited to 'lmm.h')
| -rw-r--r-- | lmm.h | 111 |
1 files changed, 0 insertions, 111 deletions
@@ -1,111 +0,0 @@ -/* - 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 <http://www.gnu.org/licenses/>. -*/ - -#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 path_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<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 - - vector<SNPINFO> snpInfo; //record SNP information - - // 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); - 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<pair<size_t, double> > &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 - - |