diff options
Diffstat (limited to 'src/ldr.h')
| -rw-r--r-- | src/ldr.h | 50 |
1 files changed, 22 insertions, 28 deletions
@@ -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 @@ -13,9 +13,8 @@ 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 __LDR_H__ #define __LDR_H__ @@ -24,25 +23,14 @@ #include <map> #include <gsl/gsl_rng.h> #include <gsl/gsl_randist.h> - -#ifdef FORCE_FLOAT -#include "param_float.h" -#else #include "param.h" -#endif - using namespace std; - - - - - class LDR { public: - // IO related parameters + // IO-related parameters. int a_mode; size_t d_pace; @@ -51,27 +39,33 @@ public: string file_out; string path_out; - // Summary statistics - size_t ni_total, ns_total; //number of total individuals and snps - size_t ni_test, ns_test; //number of individuals and snps used for analysis - size_t n_cvt; //number of covariates - 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 + // Summary statistics. + size_t ni_total, ns_total; // Total number of individuals & SNPs. + size_t ni_test, ns_test; // Number of individuals & SNPs used + // for analysis + size_t n_cvt; // Number of covariates. + + // Indicator for individuals (phenotypes): 0 missing, 1 + // available for analysis. + vector<int> indicator_idv; + + // Sequence indicator for SNPs: 0 ignored because of (a) maf, + // (b) miss, (c) non-poly; 1 available for analysis. + vector<int> indicator_snp; - vector<SNPINFO> snpInfo; //record SNP information + vector<SNPINFO> snpInfo; // Record SNP information. - // Not included in PARAM + // Not included in PARAM. gsl_rng *gsl_r; - // Main Functions + // Main functions. void CopyFromParam (PARAM &cPar); void CopyToParam (PARAM &cPar); - void VB(const vector<vector<unsigned char> > &Xt, const gsl_matrix *W_gsl, const gsl_vector *y_gsl); + void VB(const vector<vector<unsigned char> > &Xt, + const gsl_matrix *W_gsl, const gsl_vector *y_gsl); }; - - #endif |