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Diffstat (limited to 'lmm.h')
| -rw-r--r-- | lmm.h | 110 |
1 files changed, 110 insertions, 0 deletions
@@ -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 <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 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 + + |