From b3b491cd9143d33bfebd4c5b26629573afcf0970 Mon Sep 17 00:00:00 2001
From: xiangzhou
Date: Sat, 11 Jul 2015 12:57:37 -0400
Subject: add GXE test
---
src/mvlmm.h | 30 +++++++++++++++++-------------
1 file changed, 17 insertions(+), 13 deletions(-)
(limited to 'src/mvlmm.h')
diff --git a/src/mvlmm.h b/src/mvlmm.h
index 129879c..9ff567c 100644
--- a/src/mvlmm.h
+++ b/src/mvlmm.h
@@ -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 .
*/
-#ifndef __MVLMM_H__
+#ifndef __MVLMM_H__
#define __MVLMM_H__
#include "gsl/gsl_vector.h"
@@ -38,17 +38,18 @@ using namespace std;
class MVLMM {
-
+
public:
// IO related parameters
int a_mode; //analysis mode, 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;
-
+
// MVLMM related parameters
double l_min;
double l_max;
@@ -61,7 +62,7 @@ public:
size_t em_iter, nr_iter;
double em_prec, nr_prec;
size_t crt;
-
+
// Summary statistics
size_t ni_total, ni_test; //number of individuals
size_t ns_total, ns_test; //number of snps
@@ -69,22 +70,25 @@ public:
size_t n_ph;
double time_UtX; //time spent on optimization iterations
double time_opt; //time spent on optimization iterations
-
+
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 snpInfo; //record SNP information
-
+
// Not included in PARAM
vector sumStat; //Output SNPSummary Data
-
+
// Main functions
void CopyFromParam (PARAM &cPar);
void CopyToParam (PARAM &cPar);
void AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
void AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
+ void Analyzebgen (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
+ void AnalyzeBimbamGXE (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY, const gsl_vector *env);
+ void AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY, const gsl_vector *env);
void WriteFiles ();
-
+
};
void CalcMvLmmVgVeBeta (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY, const size_t em_iter, const size_t nr_iter, const double em_prec, const double nr_prec, const double l_min, const double l_max, const size_t n_region, gsl_matrix *V_g, gsl_matrix *V_e, gsl_matrix *B, gsl_matrix *se_B);
--
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