From b9758364059d52e153a9f1b4fcae3bc3f3e68422 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 7 Jul 2017 06:54:26 +0000
Subject: Fix spacing
---
src/bslmm.h | 48 ++++++++++++++++++++++++------------------------
1 file changed, 24 insertions(+), 24 deletions(-)
(limited to 'src/bslmm.h')
diff --git a/src/bslmm.h b/src/bslmm.h
index da185fa..c7768a2 100644
--- a/src/bslmm.h
+++ b/src/bslmm.h
@@ -1,22 +1,22 @@
/*
Genome-wide Efficient Mixed Model Association (GEMMA)
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
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 __BSLMM_H__
+#ifndef __BSLMM_H__
#define __BSLMM_H__
#include <vector>
@@ -30,23 +30,23 @@ using namespace std;
class BSLMM {
-public:
+public:
// IO-related parameters.
- int a_mode;
+ int a_mode;
size_t d_pace;
-
+
string file_bfile;
string file_geno;
string file_out;
string path_out;
-
+
// LMM-related parameters.
double l_min;
double l_max;
size_t n_region;
double pve_null;
double pheno_mean;
-
+
// BSLMM MCMC-related parameters
double h_min, h_max, h_scale; // Priors for h.
double rho_min, rho_max, rho_scale; // Priors for rho.
@@ -61,8 +61,8 @@ public:
size_t n_mh; // Number of MH steps per iter.
double geo_mean; // Mean of geometric dist.
long int randseed;
- double trace_G;
-
+ double trace_G;
+
HYPBSLMM cHyp_initial;
// Summary statistics.
@@ -74,32 +74,32 @@ public:
// Time spent on constructing the proposal distribution for
// gamma (i.e. lmm or lm analysis).
- double time_Proposal;
+ double time_Proposal;
// Indicator for individuals (phenotypes): 0 missing, 1
// available for analysis.
- vector<int> indicator_idv;
+ 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<int> indicator_snp;
// Record SNP information.
- vector<SNPINFO> snpInfo;
-
+ vector<SNPINFO> snpInfo;
+
// Not included in PARAM.
- gsl_rng *gsl_r;
- gsl_ran_discrete_t *gsl_t;
- map<size_t, size_t> mapRank2pos;
-
+ gsl_rng *gsl_r;
+ gsl_ran_discrete_t *gsl_t;
+ map<size_t, size_t> mapRank2pos;
+
// Main functions.
void CopyFromParam (PARAM &cPar);
void CopyToParam (PARAM &cPar);
-
+
void RidgeR(const gsl_matrix *U, const gsl_matrix *UtX,
const gsl_vector *Uty, const gsl_vector *eval,
const double lambda);
-
+
void MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
const gsl_vector *Uty, const gsl_vector *K_eval,
const gsl_vector *y);
@@ -111,10 +111,10 @@ public:
void WriteParam (const gsl_vector *alpha);
void WriteResult (const int flag, const gsl_matrix *Result_hyp,
const gsl_matrix *Result_gamma, const size_t w_col);
-
+
// Subfunctions inside MCMC.
void CalcPgamma (double *p_gammar);
-
+
double CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
const double sigma_a2);
void InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty,
--
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