1 files changed, 0 insertions, 310 deletions
diff --git a/mathfunc.cpp b/mathfunc.cpp
deleted file mode 100644
index 09e58dc..0000000
--- a/mathfunc.cpp
+++ /dev/null
@@ -1,310 +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 <http://www.gnu.org/licenses/>.
- */
-
-
-#include <iostream>
-#include <fstream>
-#include <sstream>
-#include <string>
-#include <iomanip>
-#include <bitset>
-#include <vector>
-#include <map>
-#include <set>
-#include <cstring>
-#include <cmath>
-#include <stdio.h>
-#include <stdlib.h> 
-
-#include "gsl/gsl_vector.h"
-#include "gsl/gsl_matrix.h"
-#include "gsl/gsl_linalg.h"
-#include "gsl/gsl_blas.h"
-#include "gsl/gsl_cdf.h"
-
-#ifdef FORCE_FLOAT
-#include "mathfunc_float.h"
-#else
-#include "mathfunc.h"
-#endif
-
-
-using namespace std;
-
-
-
-//calculate variance of a vector
-double VectorVar (const gsl_vector *v)
-{
-	double d, m=0.0, m2=0.0;
-	for (size_t i=0; i<v->size; ++i) {
-		d=gsl_vector_get (v, i);
-		m+=d;
-		m2+=d*d;
-	}
-	m/=(double)v->size;
-	m2/=(double)v->size;
-	return m2-m*m;
-}
-
-
-
-//center the matrix G	
-void CenterMatrix (gsl_matrix *G)
-{		
-	double d;
-	gsl_vector *w=gsl_vector_alloc (G->size1);
-	gsl_vector *Gw=gsl_vector_alloc (G->size1);
-	gsl_vector_set_all (w, 1.0);
-	
-	gsl_blas_dgemv (CblasNoTrans, 1.0, G, w, 0.0, Gw);			
-	gsl_blas_dsyr2 (CblasUpper, -1.0/(double)G->size1, Gw, w, G);
-	gsl_blas_ddot (w, Gw, &d);		
-	gsl_blas_dsyr (CblasUpper, d/((double)G->size1*(double)G->size1), w, G);
-	
-	for (size_t i=0; i<G->size1; ++i) {
-		for (size_t j=0; j<i; ++j) {
-			d=gsl_matrix_get (G, j, i);
-			gsl_matrix_set (G, i, j, d);
-		}
-	}
-	
-	gsl_vector_free(w);
-	gsl_vector_free(Gw);
-	
-	return;
-}
-
-
-//center the matrix G	
-void CenterMatrix (gsl_matrix *G, gsl_vector *w)
-{		
-	double d, wtw;
-	gsl_vector *Gw=gsl_vector_alloc (G->size1);
-	
-	gsl_blas_ddot (w, w, &wtw);	
-	gsl_blas_dgemv (CblasNoTrans, 1.0, G, w, 0.0, Gw);			
-	gsl_blas_dsyr2 (CblasUpper, -1.0/wtw, Gw, w, G);
-	gsl_blas_ddot (w, Gw, &d);		
-	gsl_blas_dsyr (CblasUpper, d/(wtw*wtw), w, G);
-	
-	for (size_t i=0; i<G->size1; ++i) {
-		for (size_t j=0; j<i; ++j) {
-			d=gsl_matrix_get (G, j, i);
-			gsl_matrix_set (G, i, j, d);
-		}
-	}
-	
-	gsl_vector_free(Gw);
-	
-	return;
-}
-
-
-//scale the matrix G such that the mean diagonal = 1
-void ScaleMatrix (gsl_matrix *G)
-{		
-	double d=0.0;
-	
-	for (size_t i=0; i<G->size1; ++i) {
-		d+=gsl_matrix_get(G, i, i);
-	}
-	d/=(double)G->size1;
-	
-	gsl_matrix_scale (G, 1.0/d);
-	
-	return;
-}
-
-
-//center the vector y
-double CenterVector (gsl_vector *y)
-{		
-	double d=0.0;
-	
-	for (size_t i=0; i<y->size; ++i) {
-		d+=gsl_vector_get (y, i);
-	}
-	d/=(double)y->size;
-	
-	gsl_vector_add_constant (y, -1.0*d);
-	
-	return d;
-}
-
-
-//calculate UtX
-void CalcUtX (const gsl_matrix *U, gsl_matrix *UtX) 
-{
-	gsl_vector *Utx_vec=gsl_vector_alloc (UtX->size1);
-	for (size_t i=0; i<UtX->size2; ++i) {
-		gsl_vector_view UtX_col=gsl_matrix_column (UtX, i);
-		gsl_blas_dgemv (CblasTrans, 1.0, U, &UtX_col.vector, 0.0, Utx_vec);
-		gsl_vector_memcpy (&UtX_col.vector, Utx_vec);
-	}	
-	gsl_vector_free (Utx_vec);
-	return;
-}
-
-
-void CalcUtX (const gsl_matrix *U, const gsl_matrix *X, gsl_matrix *UtX) 
-{
-	for (size_t i=0; i<X->size2; ++i) {
-		gsl_vector_const_view X_col=gsl_matrix_const_column (X, i);
-		gsl_vector_view UtX_col=gsl_matrix_column (UtX, i);
-		gsl_blas_dgemv (CblasTrans, 1.0, U, &X_col.vector, 0.0, &UtX_col.vector);
-	}
-	return;
-}
-
-void CalcUtX (const gsl_matrix *U, const gsl_vector *x, gsl_vector *Utx) 
-{
-	gsl_blas_dgemv (CblasTrans, 1.0, U, x, 0.0, Utx);
-	return;
-}
-
-
-//Kronecker product
-void Kronecker(const gsl_matrix *K, const gsl_matrix *V, gsl_matrix *H) 
-{
-	for (size_t i=0; i<K->size1; i++) {
-		for (size_t j=0; j<K->size2; j++) {
-			gsl_matrix_view H_sub=gsl_matrix_submatrix (H, i*V->size1, j*V->size2, V->size1, V->size2);
-			gsl_matrix_memcpy (&H_sub.matrix, V);
-			gsl_matrix_scale (&H_sub.matrix, gsl_matrix_get (K, i, j));
-		}
-	}
-	return;
-}
-
-//symmetric K matrix
-void KroneckerSym(const gsl_matrix *K, const gsl_matrix *V, gsl_matrix *H) 
-{
-	for (size_t i=0; i<K->size1; i++) {
-		for (size_t j=i; j<K->size2; j++) {
-			gsl_matrix_view H_sub=gsl_matrix_submatrix (H, i*V->size1, j*V->size2, V->size1, V->size2);
-			gsl_matrix_memcpy (&H_sub.matrix, V);
-			gsl_matrix_scale (&H_sub.matrix, gsl_matrix_get (K, i, j));
-			
-			if (i!=j) {
-				gsl_matrix_view H_sub_sym=gsl_matrix_submatrix (H, j*V->size1, i*V->size2, V->size1, V->size2);
-				gsl_matrix_memcpy (&H_sub_sym.matrix, &H_sub.matrix);
-			}
-		}
-	}
-	return;
-}
-
-
-// this function calculates HWE p value with methods described in Wigginton et al., 2005 AJHG; 
-// it is based on the code in plink 1.07
-double CalcHWE (const size_t n_hom1, const size_t n_hom2, const size_t n_ab)
-{
-	if ( (n_hom1+n_hom2+n_ab)==0 ) {return 1;}
-	
-	//aa is the rare allele
-	int n_aa=n_hom1 < n_hom2 ? n_hom1 : n_hom2;
-	int n_bb=n_hom1 < n_hom2 ? n_hom2 : n_hom1;
-	
-	int rare_copies = 2 * n_aa + n_ab;
-	int genotypes   = n_ab + n_bb + n_aa;
-	
-	double * het_probs = (double *) malloc( (rare_copies + 1) * sizeof(double));
-	if (het_probs == NULL) 
-		cout<<"Internal error: SNP-HWE: Unable to allocate array"<<endl;
-		
-		int i;
-	for (i = 0; i <= rare_copies; i++)
-		het_probs[i] = 0.0;
-		
-	/* start at midpoint */
-		int mid = rare_copies * (2 * genotypes - rare_copies) / (2 * genotypes);
-		
-	/* check to ensure that midpoint and rare alleles have same parity */
-		if ((rare_copies & 1) ^ (mid & 1))
-			mid++;
-	
-	int curr_hets = mid;
-	int curr_homr = (rare_copies - mid) / 2;
-	int curr_homc = genotypes - curr_hets - curr_homr;
-	
-	het_probs[mid] = 1.0;
-	double sum = het_probs[mid];
-	for (curr_hets = mid; curr_hets > 1; curr_hets -= 2)
-    {
-		het_probs[curr_hets - 2] = het_probs[curr_hets] * curr_hets * (curr_hets - 1.0)
-		/ (4.0 * (curr_homr + 1.0) * (curr_homc + 1.0));
-		sum += het_probs[curr_hets - 2];
-		
-		/* 2 fewer heterozygotes for next iteration -> add one rare, one common homozygote */
-		curr_homr++;
-		curr_homc++;
-    }
-	
-	curr_hets = mid;
-	curr_homr = (rare_copies - mid) / 2;
-	curr_homc = genotypes - curr_hets - curr_homr;
-	for (curr_hets = mid; curr_hets <= rare_copies - 2; curr_hets += 2)
-    {
-		het_probs[curr_hets + 2] = het_probs[curr_hets] * 4.0 * curr_homr * curr_homc
-		/((curr_hets + 2.0) * (curr_hets + 1.0));
-		sum += het_probs[curr_hets + 2];
-		
-		/* add 2 heterozygotes for next iteration -> subtract one rare, one common homozygote */
-		curr_homr--;
-		curr_homc--;
-    }
-	
-	for (i = 0; i <= rare_copies; i++)
-		het_probs[i] /= sum;
-		
-	/* alternate p-value calculation for p_hi/p_lo
-	 double p_hi = het_probs[n_ab];
-	 for (i = n_ab + 1; i <= rare_copies; i++)
-     p_hi += het_probs[i];
-	 
-	 double p_lo = het_probs[n_ab];
-	 for (i = n_ab - 1; i >= 0; i--)
-	 p_lo += het_probs[i];
-	 
-	 double p_hi_lo = p_hi < p_lo ? 2.0 * p_hi : 2.0 * p_lo;
-	 */
-		
-		double p_hwe = 0.0;
-	/*  p-value calculation for p_hwe  */
-		for (i = 0; i <= rare_copies; i++)
-		{
-			if (het_probs[i] > het_probs[n_ab])
-				continue;
-			p_hwe += het_probs[i];
-		}
-	
-	p_hwe = p_hwe > 1.0 ? 1.0 : p_hwe;
-	
-	free(het_probs);
-	
-	return p_hwe;
-}
-
-
-
-
-
-
-	
-