From 9aa9f76cb16a0e71fea19dd125761034aaca4fd4 Mon Sep 17 00:00:00 2001
From: xiangzhou
Date: Mon, 22 Sep 2014 11:12:46 -0400
Subject: version 0.95alpha
---
lm.h | 75 --------------------------------------------------------------------
1 file changed, 75 deletions(-)
delete mode 100644 lm.h
(limited to 'lm.h')
diff --git a/lm.h b/lm.h
deleted file mode 100644
index ceec060..0000000
--- a/lm.h
+++ /dev/null
@@ -1,75 +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 __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
-
- string file_bfile;
- string file_geno;
- string file_out;
- string path_out;
-
- 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
- size_t n_cvt;
- double time_opt; //time spent
-
- 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 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);
- void WriteFiles ();
-};
-void MatrixCalcLmLR (const gsl_matrix *X, const gsl_vector *y, vector > &pos_loglr);
-#endif
--
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