From 9aa9f76cb16a0e71fea19dd125761034aaca4fd4 Mon Sep 17 00:00:00 2001 From: xiangzhou Date: Mon, 22 Sep 2014 11:12:46 -0400 Subject: version 0.95alpha --- param.h | 232 ---------------------------------------------------------------- 1 file changed, 232 deletions(-) delete mode 100644 param.h (limited to 'param.h') diff --git a/param.h b/param.h deleted file mode 100644 index fa18181..0000000 --- a/param.h +++ /dev/null @@ -1,232 +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 . -*/ - -#ifndef __PARAM_H__ -#define __PARAM_H__ - -#include -#include -#include -#include "gsl/gsl_vector.h" -#include "gsl/gsl_matrix.h" - -using namespace std; - - - -class SNPINFO { -public: - string chr; - string rs_number; - double cM; - long int base_position; - string a_minor; - string a_major; - size_t n_miss; - double missingness; - double maf; -}; - -//results for lmm -class SUMSTAT { -public: - double beta; //REML estimator for beta - double se; //SE for beta - double lambda_remle; //REML estimator for lambda - double lambda_mle; //MLE estimator for lambda - double p_wald; //p value from a Wald test - double p_lrt; //p value from a likelihood ratio test - double p_score; //p value from a score test -}; - -//results for mvlmm -class MPHSUMSTAT { -public: - vector v_beta; //REML estimator for beta - double p_wald; //p value from a Wald test - double p_lrt; //p value from a likelihood ratio test - double p_score; //p value from a score test - vector v_Vg; //estimator for Vg, right half - vector v_Ve; //estimator for Ve, right half - vector v_Vbeta; //estimator for Vbeta, right half -}; - - -//hyper-parameters for bslmm -class HYPBSLMM { -public: - double h; - double pve; - double rho; - double pge; - double logp; - - size_t n_gamma; -}; - - - - -class PARAM { -public: - // IO related parameters - bool mode_silence; - int a_mode; //analysis mode, 1/2/3/4 for Frequentist tests - int k_mode; //kinship read mode: 1: n by n matrix, 2: id/id/k_value; - vector p_column; //which phenotype column needs analysis - size_t d_pace; //display pace - - string file_bfile; - string file_geno; - string file_pheno; - string file_anno; //optional - string file_cvt; //optional - string file_kin; - string file_ku, file_kd; - string file_mk; - string file_out; - string path_out; - - string file_epm; //estimated parameter file - string file_ebv; //estimated breeding value file - string file_log; //log file containing mean estimate - - string file_read; //file containing total number of reads - string file_gene; //gene expression file - - string file_snps; //file containing analyzed snps or genes - - - - // QC related parameters - double miss_level; - double maf_level; - double hwe_level; - double r2_level; - - // LMM related parameters - double l_min; - double l_max; - size_t n_region; - double l_mle_null, l_remle_null; - double logl_mle_H0, logl_remle_H0; - double pve_null, pve_se_null; - double vg_remle_null, ve_remle_null, vg_mle_null, ve_mle_null; - vector Vg_remle_null, Ve_remle_null, Vg_mle_null, Ve_mle_null; - vector VVg_remle_null, VVe_remle_null, VVg_mle_null, VVe_mle_null; - vector beta_remle_null, se_beta_remle_null, beta_mle_null, se_beta_mle_null; - double p_nr; - double em_prec, nr_prec; - size_t em_iter, nr_iter; - size_t crt; - double pheno_mean; //phenotype mean from bslmm fitting or for prediction - - //for fitting multiple variance components - //the first three are of size n_vc, and the next two are of size n_vc+1 - vector v_traceG; - vector v_pve; - vector v_se_pve; - - vector v_sigma2; - vector v_se_sigma2; - vector v_beta; - vector v_se_beta; - - // BSLMM MCMC related parameters - double h_min, h_max, h_scale; //priors for h - double rho_min, rho_max, rho_scale; //priors for rho - double logp_min, logp_max, logp_scale; //priors for log(pi) - size_t s_min, s_max; //minimum and maximum number of gammas - size_t w_step; //number of warm up/burn in iterations - size_t s_step; //number of sampling iterations - size_t r_pace; //record pace - size_t w_pace; //write pace - size_t n_accept; //number of acceptance - size_t n_mh; //number of MH steps within each iteration - double geo_mean; //mean of the geometric distribution - long int randseed; - double trace_G; - - HYPBSLMM cHyp_initial; - - // Summary statistics - bool error; - size_t ni_total, ni_test, ni_cvt; //number of individuals - size_t np_obs, np_miss; //number of observed and missing phenotypes - size_t ns_total, ns_test; //number of snps - size_t ng_total, ng_test; //number of genes - size_t ni_control, ni_case; //number of controls and number of cases - size_t n_cvt; //number of covariates - size_t n_ph; //number of phenotypes - size_t n_vc; //number of variance components (including the diagonal matrix) - double time_total; //record total time - double time_G; //time spent on reading files the second time and calculate K - double time_eigen; //time spent on eigen-decomposition - double time_UtX; //time spent on calculating UX and Uy - double time_UtZ; //time spent on calculating UtZ, for probit BSLMM - double time_opt; //time spent on optimization iterations/or mcmc - double time_Omega; //time spent on calculating Omega - double time_hyp; //time spent on sampling hyper-parameters, in PMM - double time_Proposal; //time spend on constructing the proposal distribution (i.e. the initial lmm or lm analysis) - - // Data - vector > pheno; //a vector record all phenotypes, NA replaced with -9 - vector > cvt; //a vector record all covariates, NA replaced with -9 - vector > indicator_pheno; //a matrix record when a phenotype is missing for an individual; 0 missing, 1 available - vector indicator_idv; //indicator for individuals (phenotypes), 0 missing, 1 available for analysis - vector indicator_snp; //sequence indicator for SNPs: 0 ignored because of (a) maf, (b) miss, (c) non-poly; 1 available for analysis - vector indicator_cvt; //indicator for covariates, 0 missing, 1 available for analysis - - vector indicator_bv; //indicator for estimated breeding value file, 0 missing, 1 available for analysis - vector indicator_read; //indicator for read file, 0 missing, 1 available for analysis - vector vec_read; //total number of reads - vector vec_bv; //breeding values - vector est_column; - - map mapID2num; //map small ID number to number, from 0 to n-1 - map mapRS2chr; //map rs# to chromosome location - map mapRS2bp; //map rs# to base position - map mapRS2cM; //map rs# to cM - map mapRS2est; //map rs# to parameters - - vector snpInfo; //record SNP information - set setSnps; //a set of snps for analysis - - //constructor - PARAM(); - - //functions - void ReadFiles (); - void CheckParam (); - void CheckData (); - void PrintSummary (); - void ReadGenotypes (gsl_matrix *UtX, gsl_matrix *K, const bool calc_K); - void CheckCvt (); - void CopyCvt (gsl_matrix *W); - void ProcessCvtPhen(); - void CopyCvtPhen (gsl_matrix *W, gsl_vector *y, size_t flag); - void CopyCvtPhen (gsl_matrix *W, gsl_matrix *Y, size_t flag); - void CalcKin (gsl_matrix *matrix_kin); - void WriteMatrix (const gsl_matrix *matrix_U, const string suffix); - void WriteVector (const gsl_vector *vector_D, const string suffix); - void CopyRead (gsl_vector *log_N); -}; - - -#endif - -- cgit v1.2.3