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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2008 Shaun Purcell //
// //
// This file is distributed under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#ifndef __SETS_H__
#define __SETS_H__
class SetSortedSNP
{
public:
double chisq;
int l;
bool operator< (const SetSortedSNP & s2) const
{ return (chisq < s2.chisq); }
};
class Set
{
public:
vector<int> s_min;
vector<int> s_max;
Set(vector<vector<int> > &);
vector<vector<int> > & snpset;
map<int,set<int> > setMapping;
// Sum-statistics based set-based scores
void empiricalSetPValues();
void cumulativeSetSum_WITHOUTLABELS(vector<double>&,int);
void cumulativeSetSum_WITHLABELS(Plink &, vector<double>&);
// Profile-score based set-based tests
void initialiseSetMapping();
void profileTestSNPInformation(int,double);
vector_t profileTestScore();
void profileTestInitialise();
vector<vector<int> > profileSNPs;
vector<vector_t> profileScore;
// Stepwise regression models
vector_t fitStepwiseModel();
// New, LD-aware single-statistic set test
vector_t fitLDSetTest(vector_t&,bool);
vector< vector<set<int> > > ldSet;
vector<int> numSig;
vector<vector<int> > selectedSNPs;
// Helper functions
void sizeSets();
void pruneSets(Plink&);
void pruneMC(Plink &,bool,double);
void dropNotSet(Plink &);
void makeLDSets();
// get better name ??
vector<vector<string> > setsort;
// All statistics
vector<vector<vector<double> > > stat_set;
// Empirical set-based p-values (p0, p1 and p2)
vector<vector<vector<double> > > pv_set;
vector<vector<double> > pv_maxG_set;
vector<vector<double> > pv_maxE_set;
// Include or drop this SNP (multi-collinearity)
vector<vector<bool> > cur;
};
#endif
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