diff options
Diffstat (limited to 'src/lm.h')
| -rw-r--r-- | src/lm.h | 54 |
1 files changed, 27 insertions, 27 deletions
diff --git a/src/lm.h b/src/lm.h index 656dd52..fac84e1 100644 --- a/src/lm.h +++ b/src/lm.h @@ -1,6 +1,6 @@ /* Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011 Xiang Zhou + 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 @@ -13,33 +13,25 @@ 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 __LM_H__ #define __LM_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 LM { public: - // IO related parameters - int a_mode; //analysis mode, 50+1/2/3/4 for Frequentist tests - size_t d_pace; //display pace + // 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; @@ -49,31 +41,39 @@ public: 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 + // 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 + 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 + // 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 *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 + // 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); + +void MatrixCalcLmLR (const gsl_matrix *X, const gsl_vector *y, + vector<pair<size_t, double> > &pos_loglr); + #endif |