diff options
Diffstat (limited to 'src/lm.h')
| -rw-r--r-- | src/lm.h | 28 |
1 files changed, 16 insertions, 12 deletions
@@ -1,22 +1,22 @@ /* 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 __LM_H__ +#ifndef __LM_H__ #define __LM_H__ #include "gsl/gsl_vector.h" @@ -35,40 +35,44 @@ using namespace std; class LM { - + public: // IO related parameters int a_mode; //analysis mode, 50+1/2/3/4 for Frequentist tests size_t d_pace; //display pace - + string file_bfile; string file_geno; + string file_oxford; string file_out; string path_out; - + string file_gene; - + // 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_opt; //time spent - + 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 *W, const gsl_vector *x); void AnalyzePlink (const gsl_matrix *W, const gsl_vector *y); void AnalyzeBimbam (const gsl_matrix *W, const gsl_vector *y); + // WJA added + void Analyzebgen (const gsl_matrix *W, const gsl_vector *y); + void WriteFiles (); }; void MatrixCalcLmLR (const gsl_matrix *X, const gsl_vector *y, vector<pair<size_t, double> > &pos_loglr); |