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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2009 Shaun Purcell //
// //
// This file is distributed under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#ifndef __MODEL_H__
#define __MODEL_H__
#include<vector>
#include "plink.h"
using namespace std;
class Model {
public:
Model();
virtual ~Model() { };
virtual void setDependent() = 0;
virtual void pruneY() = 0;
virtual void fitLM() = 0;
virtual vector_t getCoefs() = 0;
virtual vector_t getVar() = 0;
virtual vector_t getSE() = 0;
virtual vector_t getPVals() = 0;
virtual void displayResults(ofstream &, Locus *) = 0;
virtual void fitUnivariateLM() = 0;
void setMissing();
vector<bool> getMissing();
void setMissing(vector<bool>&);
void yokeMissing(Model *);
void setHaploid();
void setX();
void setDominant();
void setRecessive();
void hasSNPs(bool);
void addAdditiveSNP(int);
void addDominanceSNP(int);
void addHaplotypeDosage(set<int>&);
void addSexEffect();
bool isSexInModel();
void addCovariate(int);
void addInteraction(int,int);
void buildDesignMatrix();
bool checkVIF();
vector<bool> validParameters();
bool isValid() { return all_valid; }
double getStatistic();
// double getPValue();
double linearHypothesis(matrix_t &, vector_t &);
int Ysize() { return nind; }
int getNP() { return np; }
void setValid() { all_valid = true; }
vector<string> label;
vector<int> order;
vector<int> type;
int testParameter;
void noCluster();
void setCluster();
virtual void HuberWhite() = 0;
// Independent variables (can be directly manipulated...)
vector<vector<double> > X;
protected:
Plink * P;
// Missing flag
vector<bool> miss;
int nind;
int np; // Main effects + interaction + intercept
bool has_snps;
vector<bool> xchr;
vector<bool> haploid;
bool sex_effect;
vector<bool> valid;
bool all_valid;
vector_t coef; // beta
matrix_t S; // Sigma
// Term types
enum terms { INTERCEPT,
ADDITIVE,
DOMDEV,
HAPLOTYPE,
SEX,
COVARIATE,
INTERACTION,
QFAM };
double buildIntercept();
double buildAdditive(Individual *, int);
double buildDominance(Individual *, int);
double buildHaplotype(int, int);
double buildSex(Individual *);
double buildCovariate(Individual *, int);
double buildInteraction(Individual *, int, vector_t &);
double buildQFAM(Individual *);
bool skip;
// List of additive SNP effects
// assuming SNP major mode
vector<int> additive;
int mAA;
int mAB;
int mBB;
double mA, mB;
// List of dominance deviation SNP effects
vector<int> dominance;
// List of covariates (clist)
vector<int> covariate;
// List of pairwise interactions
// ( indexing previously specified components, 1,2,..)
vector<int2> interaction;
// List of sets of haplotypes
vector<set<int> > haplotype;
// Clustering information
bool cluster;
vector<int> clst;
int nc;
};
#endif
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