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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2007 Shaun Purcell //
// //
// This file is distributed under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#ifndef CLUMP_LD_H_
#define CLUMP_LD_H_
#include <string>
#include <vector>
#include <map>
#include "plink.h"
#include "helper.h"
using namespace std;
class ResultTrio
{
public:
double p; // p-value
string annot; // Annotation
int f; // which results file?
string s; // SNP name
bool operator< (const ResultTrio & p2) const
{
return ( p < p2.p );
}
};
class ClumpPair {
public:
string snp;
int f;
bool operator< (const ClumpPair & p2) const
{
if ( snp == p2.snp ) return ( f < p2.f );
return ( snp < p2.snp );
}
};
class ClumpResults {
public:
double p;
string annot;
bool operator< (const ClumpResults & p2) const
{
return ( p < p2.p );
}
};
class clump_LD
{
public:
Plink * P;
HaploPhase * hp;
//will be user defined
double pval_cutoff;
double ld_distance;
double second_pval_cutoff;
float r2_cutoff;
map<string, bool> clumped;
vector<string> snps;
vector<double> pvals;
map<ClumpPair, ClumpResults> assoc_results;
vector<string> filename;
// constructer
clump_LD(Plink*,HaploPhase*,
double, double, double, float);
// accessors
void set_pval( double );
void set_second_pval( double );
void set_ld( double );
void set_r2( double );
// methods
vector<ResultTrio> read_assoc_file(string);
void clump();
string allelePairs(int,int);
};
#endif /*CLUMP_LD_H_*/
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