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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2006 Shaun Purcell //
// //
// This file is distributed under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#ifndef __PERM_H__
#define __PERM_H__
#include "options.h"
using namespace std;
class Perm {
int t; // Number of tests
long int replicates; // Basic number of replicates
long int performed; // Number of replicates actually performed
bool count; // Output counts, not p-values
ofstream PDUMP; // Verbose permutation dump
bool dump_best; // Record just best permutation result
bool dump_all; // Record all permutation results
vector<int> order; // For --rank, record order of original
vector<int> reorder; // For --rank, record order of original, reverse mapping
/////////////////////////////
// Gene-dropping permutation
bool genedrop;
map<Individual*,int> idmap;
///////////////////////////////////////////
// Standard phenotype-swapping permutation
// Parameters for adaptive permutation
bool adaptive;
int min; // Minimum number of permutations
double zt; // SD CI range (based on par::adaptive_alpha)
int interval; // Prune tests every (I+N*I2) permutations
// Main storage
vector<int> R; // number of successes
vector<int> maxR; // number of genome-wide successes
vector<long int> N; // number of trials (adaptive)
// Cluster information
vector< vector<int> > s;
int ns; // number of clusters
Plink & P; // reference to Plink class
public:
Perm(Plink &);
void closeDUMP()
{
if (dump_all || dump_best)
PDUMP.close();
}
// For basic permutation
vector<int> pheno; // label-swapped phenotype
vector<int> geno; // label-swapped phenotype
vector<bool> test; // whether to stop with this test
vector<bool> snp_test; // whether to skip these SNPs in
// a set-based test
void setTests(int x);
void setAdaptiveSetSNPs(int x);
void originalOrder();
void setOriginalRanking(vector_t&);
bool finished();
bool update(vector<double>&, vector<double>&);
bool updateSNP(double,double,int);
void nextSNP();
vector<double> & report();
int current_reps() { return performed; }
int reps_done(int);
double pvalue(int);
double max_pvalue(int);
int rank(int);
void permuteInCluster();
void setPermClusters(Plink &);
void preGeneDrop();
void geneDrop();
void dropAlleles(Plink &,
Individual*,
int,
int,
vector<bool>&,
vector<bool>&,
vector<bool>&,
map<Individual*,int> &);
};
#endif
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