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matvec::Individual Class Reference

#include <individual.h>

List of all members.

Detailed Description

an individual consists of genomes

See also:: Genome

Definition at line 112 of file individual.h.

Public Methods

Individual (void)

Individual (Population *P)

Individual (const Individual &A)

~Individual (void)

const Individual & operator= (const Individual &A)

int terminal () const

int base () const

int isolated () const

void reset_id (const unsigned newid)

void release (void)

void remodel (Population *P)

void gamete (Chromosome *C, const int n, const double r) const

void display ()

void save (std::ostream &out)

void xbzu (const double x)

void initial_anterior (const double *gfreq, const unsigned tng, const int cond=-1)

void initial_posterior (const unsigned tng, const int cond=-1)

void pretend_missing (int on, const double *gfreq, const unsigned tng)

void setPenetrance (penetranceType p)

double get_penetrance (Vector< double > &pen)

double xbzu (void) const

double genotypic_val (void) const

double inbcoef (void) const

double father_inbcoef (void) const

double mother_inbcoef (void) const

unsigned nchrom (void) const

unsigned family_id (void)

unsigned marked (void) const

unsigned id (void) const

unsigned nspouse (void) const

unsigned noffs (void) const

const unsigned * noffs_spouse (void) const

char sex (void) const

unsigned gid (void) const

unsigned paternal_chrom_id (const unsigned c) const

unsigned maternal_chrom_id (const unsigned c) const

unsigned father_id (void) const

unsigned mother_id (void) const

unsigned father_gid (void) const

unsigned mother_gid (void) const

DataNode * record (void) const

Chromosome * paternal_chrom (void)

Chromosome * maternal_chrom (void)

Individual * father (void) const

Individual * mother (void) const

Individual ** offspring (void) const

Individual ** spouses (void) const

void genotype (const unsigned c, const unsigned l, unsigned gtype[]) const

void set_genotype (const unsigned c, const unsigned l, const unsigned a0, const unsigned a1)

void set_switch (int Nloci)

void initial_multi_anterior (doubleMatrix &penetrance)

void initial_multi_posterior (const int cond)

void collapse_antpost (void)

unsigned n_switches (void)

double get_m_penetrance (doubleMatrix &pen)

void pretend_multi_missing (int on, doubleMatrix &pen)

void put_family (int i)

int get_family (void)

void cal_gprobs (Dblock &post_mat_f)

Vector< double > get_gprobs (void)

double get_m_posterior (int excJ,Dblock &post_mat)

void initial_multi_m_posterior (const unsigned tn_qtl, const int cond)

void initial_multi_m_anterior (const unsigned tn_qtl)

void pretend_multi_m_missing (int on, int tng)

void cal_m_gprobs (int tng)

void collapse_mix_antpost (void)

double get_mix_penetrance (Vector< double > &pen)

void put_gametes (Vector< unsigned > m_g, Vector< unsigned > p_g)

void set_founder_alleles (bool)

Vector< unsigned > & get_founder (std::string, bool)

void update_offsprings_founder_alleles (void)

void t0 (unsigned SLlocus, unsigned gender_parent)

void t1 (unsigned SLlocus)

void t2a (unsigned SLlocus)

void t2b (unsigned SLlocus)

void apply_SL_transition (const unsigned rule, const unsigned lcs)

void apply_SL_cascade (const unsigned rule, const unsigned SLlocus)

double graph_trans_prob (unsigned, unsigned, unsigned)

double calc_q (void)

method to calc q prob for individual; q is stored in 1 variable

void sample_haplotypes (const unsigned)

void sample_self (int parent_indicator)

Vector< unsigned > get_id_pdq (void)

void search_heteroz (unsigned qtl)

void get_allele_v1 (unsigned lcs, Vector< int > allele_vector1)

void count_haplotype (void)

void display_freq_haplotype (unsigned)

void map_pdq (int samples, int interval, double r_aq, double r_bq)

void map_pdq (int samples, int interval, BG r_aq, BG r_bq)

void parents (void)

unsigned allAllelesForLocus (unsigned j)

unsigned allGenosForLocus (unsigned j)

double getAllelePenetrance (void)

returns the allele penetrance for the RSampler

double getDisAllelePenetrance (void)

double getAllelePenetrance (unsigned forLocus)

double getDisAllelePenetrance (unsigned forLocus)

double getGenoPenetrance (void)

returns the genotype penetrance for the RSampler

double getDisGenoPenetrance (void)

double getAlleleMTransmissionProb (void)

returns the transmission probability of a maternal allele when the allele origin is assumed known. Used when we peel across pedigree and loci jointly.

double getAllelePTransmissionProb (void)

returns the transmission probability of a paternal allele when the allele origin is assumed known. Used when we peel across pedigree and loci jointly.

double getAlleleMRTransmissionProb (unsigned forLocus)

double getAllelePRTransmissionProb (unsigned forLocus)

double getTransitionProb (void)

returns the genotype transition probability in the RSampler

double getMTransmissionProb (void)

returns the maternal allele transmission probability for the RSampler for genotype peeling

double getPTransmissionProb (void)

returns the paternal allele transmission probability for the RSampler for genotype peeling

double getTransmissionProb (unsigned iA, unsigned mA, unsigned pA, Vector< unsigned > &gamete)

double getMatthiasTransitionProb (void)

double getMatthiasMTransmissionProb (void)

double getMatthiasPTransmissionProb (void)

double getMatthiasTransmissionProb (unsigned iA, unsigned mA, unsigned pA, Vector< unsigned > &gamete, Vector< unsigned > &gameteOld)

int findLeftLocus (Vector< unsigned > &gamete)

int findRightLocus (Vector< unsigned > &gamete)

void setFounderHaplotype (void)

makes sure that in founders the maternal allele is asigned the lower allele state

void displayGenotypes (unsigned locus)

void displayAlleleVectors (unsigned locus)

void setAlleleStateVectors (unsigned locus)

void setAlleleOriginVectors (unsigned locus)

Public Attributes

int loop_connector

int p_origin

unsigned group_id

int genotype_id

double RBV

double MBV

double est_GV

double true_GV

double xbzu_val

DataNode * myrecord

Vector< double > anterior

Vector< double > * posterior

Vector< double > posterior_iw

double anterior_iw

doubleMatrix * residual_var

int m_anterior_iw

Dblock m_anterior

Vector< Dblock > m_posterior

double m_anterior_scale

Vector< double > m_posterior_scale

Vector< Vector< UNormal > > mix_anterior

Vector< Mixed_post_vec > mix_posterior

Vector< unsigned > m_gamete

Vector< unsigned > m_gamete1

Vector< unsigned > p_gamete

Vector< unsigned > p_gamete1

Vector< unsigned > m_founder

Vector< unsigned > p_founder

unsigned p_counter

unsigned m_counter

int marker_index

double q_prob

doubleMatrix genotype_freq1

doubleMatrix genotype_freq2

int *** mode_matrix

int assigned_founder_allele

Vector< unsigned > id_pdq

Vector< unsigned > id_pdq1

unsigned ord_heter

unsigned initial_order1

unsigned initial_order2

Matrix< unsigned > m_haplotype

Matrix< unsigned > p_haplotype

double mm_pdq

double mp_pdq

double pm_pdq

double pp_pdq

BG bgDMPDQ

BG bgSMPDQ

Vector< unsigned > m_counter_map

Vector< unsigned > p_counter_map

SafeSTLVector< unsigned > matHaplotypeCount

SafeSTLVector< unsigned > patHaplotypeCount

Vector< unsigned > m_gameteOld

Vector< unsigned > p_gameteOld

SafeSTLVector< GenotypeNode > genotNodeVector

SafeSTLVector< AlleleStateNode > malleleStateNodeVector

SafeSTLVector< AlleleStateNode > palleleStateNodeVector

SafeSTLVector< AlleleOriginNode > malleleOriginNodeVector

SafeSTLVector< AlleleOriginNode > palleleOriginNodeVector

Vector< Vector< double > > mHaplotypeFreq

Vector< Vector< double > > pHaplotypeFreq

Static Public Attributes

Population * population

doubleMatrix g_weight

std::vector< std::vector<
double > > vec_prob

std::vector< std::vector<
double > > vec_cutsetval

SafeSTLVector< unsigned > QTLPosVector

unsigned numLoci

unsigned currentLocus

unsigned nQTL

double isqrt2pi = 1.0/std::sqrt(6.283185308)

Protected Methods

void copyfrom (const Individual &A)

Protected Attributes

unsigned myid

unsigned numchrom

unsigned numoffs

unsigned numspouse

unsigned numtrait

unsigned * numoffs_spouse

Individual * myfather

Individual * mymother

Individual ** myoffspring

Individual ** spouselist

penetranceType penetrance_f

char mysex

int connect_keeper

int index_sw

int bet_sw

int eps_sw

int family

Vector< double > gprobs

double inbc

Genome genome0

Genome genome1

Vector< double > * genotype_counter

std::set< Individual * > offs_tree

std::list< NuFamily * > related_family

Friends

class Population

class NuFamily

ostream & operator<< (ostream &stream, Individual &i)

Constructor & Destructor Documentation

matvec::Individual::Individual ( void )

Definition at line 88 of file individual.cpp.
References assigned_founder_allele, connect_keeper, est_GV, genotype_counter, genotype_id, group_id, inbc, loop_connector, marker_index, MBV, myid, myoffspring, myrecord, mysex, numchrom, numoffs_spouse, numtrait, p_origin, population, posterior, RBV, residual_var, spouselist, true_GV, and xbzu_val.

00089 { 00090 population = 0; 00091 genotype_id = -1; 00092 myid = 0; 00093 mysex = '.'; // Changed from zero 00094 numtrait = 0; 00095 numchrom = 0; 00096 myrecord = 0; 00097 posterior = 0; 00098 p_origin = 1; 00099 RBV = 0.0; 00100 MBV = 0.0; 00101 inbc = 0.0; 00102 est_GV = 0.0; 00103 true_GV = 0.0; 00104 xbzu_val = 0.0; 00105 group_id = 0; 00106 spouselist = 0; 00107 myoffspring = 0; 00108 residual_var = 0; 00109 loop_connector = 0; 00110 connect_keeper = 0; 00111 numoffs_spouse = 0; 00112 genotype_counter = 0; 00113 marker_index = 0; 00114 assigned_founder_allele = 0; 00115 }

matvec::Individual::Individual ( Population * P )

Definition at line 117 of file individual.cpp.
References assigned_founder_allele, connect_keeper, est_GV, genotype_counter, genotype_id, group_id, inbc, loop_connector, marker_index, MBV, myid, myoffspring, myrecord, mysex, numoffs_spouse, p_origin, population, posterior, RBV, remodel(), residual_var, spouselist, true_GV, and xbzu_val.

00118 { 00119 if (population == P) return; 00120 population = P; 00121 genotype_id = -1; 00122 myid = 0; 00123 mysex = '.'; 00124 myrecord = 0; 00125 posterior = 0; 00126 p_origin = 1; 00127 RBV = 0.0; 00128 MBV = 0.0; 00129 inbc = 0.0; 00130 est_GV = 0.0; 00131 true_GV = 0.0; 00132 xbzu_val = 0.0; 00133 group_id = 0; 00134 00135 spouselist = 0; 00136 myoffspring = 0; 00137 residual_var = 0; 00138 loop_connector = 0; 00139 connect_keeper = 0; 00140 numoffs_spouse = 0; 00141 genotype_counter = 0; 00142 marker_index = 0; 00143 assigned_founder_allele = 0; 00144 remodel(P); 00145 }

matvec::Individual::Individual ( const Individual & A )

Definition at line 147 of file individual.cpp.
References assigned_founder_allele, copyfrom(), myoffspring, myrecord, numoffs, numoffs_spouse, posterior, and spouselist.

00148 { 00149 numoffs = 0; 00150 myrecord = 0; 00151 posterior = 0; 00152 myoffspring = 0; 00153 spouselist = 0; 00154 numoffs_spouse = 0; 00155 copyfrom(A); 00156 assigned_founder_allele = 0; 00157 }

matvec::Individual::~Individual ( void ) [inline]

Definition at line 154 of file individual.h.
References release().

00154 {release();}

Member Function Documentation

unsigned matvec::Individual::allAllelesForLocus ( unsigned j )

unsigned matvec::Individual::allGenosForLocus ( unsigned j )

void matvec::Individual::apply_SL_cascade ( const unsigned rule,

const unsigned SLlocus

)

Definition at line 1584 of file individual.cpp.
References apply_SL_transition(), m_gamete, population, matvec::ranf(), matvec::Population::RecoVector, and matvec::Vector< unsigned >::size().
Referenced by matvec::Population::M_H_sample_ext().

01584 { 01585 //going from SL locus, we apply SL to the other loci depending on distance 01586 //first, go from SLlocus down to locus 1 01587 unsigned rule_applied = 1; 01588 for (unsigned locus = SLlocus - 1; locus > 0; locus--) { 01589 double u = ranf(); 01590 if ((u > population->RecoVector(locus) && rule_applied) || 01591 (u < population->RecoVector(locus) && !rule_applied)) { 01592 //apply T rule 01593 apply_SL_transition(rule, locus); 01594 rule_applied = 1; 01595 } 01596 else { 01597 rule_applied = 0; 01598 } 01599 } 01600 01601 //then go from SLlocus up to last locus 01602 rule_applied = 1; 01603 for (unsigned locus = SLlocus; locus < m_gamete.size(); locus++) { 01604 double u = ranf(); 01605 if ((u > population->RecoVector(locus) && rule_applied) || 01606 (u < population->RecoVector(locus) && !rule_applied)) { 01607 //apply T rule 01608 apply_SL_transition(rule, locus + 1); 01609 rule_applied = 1; 01610 } 01611 else { 01612 rule_applied = 0; 01613 } 01614 } 01615 return; 01616 }

void matvec::Individual::apply_SL_transition ( const unsigned rule,

const unsigned lcs

)

Definition at line 1559 of file individual.cpp.
References matvec::ranf(), t0(), t1(), t2a(), and t2b().
Referenced by apply_SL_cascade(), and matvec::Population::M_H_sample_ext().

01559 { 01560 if (rule > 3) { 01561 throw exception("Population::apply_SL_transition: nonexistent rule!, abort"); 01562 } 01563 switch (rule) { 01564 case 0: { //T0 rule 01565 t0(locus,unsigned(ranf()*2)); //choose gender at random 01566 break; 01567 } 01568 case 1: { //T1 rule 01569 t1(locus); 01570 break; 01571 } 01572 case 2: { //T2a rule 01573 t2a(locus); 01574 break; 01575 } 01576 case 3: { //T2b rule 01577 t2b(locus); 01578 break; 01579 } 01580 } 01581 return; 01582 }

int matvec::Individual::base ( ) const [inline]

Definition at line 159 of file individual.h.
Referenced by matvec::Population::calc_prior_descent_graph(), matvec::Population::genotype_dist_peeling(), matvec::NuFamily::multi_ant_post(), matvec::NuFamily::multi_m_ant_post(), matvec::Population::nbase(), matvec::Population::output_pdq(), and matvec::Population::partial_iterative_peeling().

00159 {return !(myfather || mymother);}

void matvec::Individual::cal_gprobs ( Dblock & post_mat_f )

Definition at line 905 of file individual.cpp.
References get_m_posterior(), matvec::Dblock::get_ndim(), gprobs, m_anterior, n_switches(), and matvec::Vector< double >::resize().
Referenced by matvec::Population::multi_geno_dist_peeling().

00905 { 00906 double val; 00907 int ii,jj,kk; 00908 00909 get_m_posterior(-1,post_mat_f); 00910 gprobs.resize(4); 00911 val = 0; 00912 for (jj=0;jj<4; jj++) { 00913 for (kk=0; kk < post_mat_f.get_ndim() ; kk++) { 00914 for (ii=0;ii< n_switches(); ii++) { 00915 gprobs[jj] += post_mat_f[kk][ii][jj]*m_anterior[kk][ii][jj]; 00916 } 00917 } 00918 val += gprobs[jj]; 00919 } 00920 for (jj=0; jj<4; jj++) { 00921 gprobs[jj] /= val; 00922 } 00923 }

void matvec::Individual::cal_m_gprobs ( int tng )

Definition at line 1047 of file individual.cpp.
References matvec::DataNode::double_val(), g_weight, gprobs, matvec::Population::mean_for_genotype, matvec::DataNode::missing, mix_anterior, mix_posterior, n_switches(), nspouse(), population, record(), residual_var, and matvec::Vector< double >::resize().
Referenced by matvec::Population::multi_m_geno_dist_peeling().

01047 { 01048 double val,y,v_y,k_y,nu_y, a11, a12, a22, k, v, nu, inverse_sqrt2pi, sum1, sum2; 01049 int i_q, i_sw, i_sp, i_switches,j; 01050 i_switches=n_switches(); 01051 inverse_sqrt2pi = 1.0/std::sqrt(4.0*std::asin(1.0)); // pi = 2.0*std::asin(1.0) 01052 gprobs.resize(tng); 01053 val = 0.0; 01054 sum1=0.0; 01055 for (i_q=0;i_q<tng;i_q++){ 01056 // contributions from penetrance function 01057 // skip if phenotype if missing 01058 01059 if (!(record()[0].missing)) { 01060 y = record()[0].double_val(); 01061 v_y = 1.0/(*residual_var[0][0]); 01062 k_y = std::log(inverse_sqrt2pi*std::sqrt(v_y)); 01063 nu_y = population->mean_for_genotype[i_q] - y; 01064 } 01065 else{ 01066 nu_y = 0.0; 01067 v_y = 0.0; 01068 k_y = 0.0; 01069 } 01070 01071 for (i_sw=0; i_sw < i_switches; i_sw++){ // loop for genotypes of J 01072 01073 a11 = nu_y*nu_y*v_y; 01074 a12 = nu_y*v_y; 01075 a22 = v_y; 01076 k = k_y; 01077 // contributions from anterior 01078 01079 v = mix_anterior[i_q][i_sw].tsq; 01080 nu = mix_anterior[i_q][i_sw].nu; 01081 k += mix_anterior[i_q][i_sw].k; 01082 a11 += nu*nu*v; 01083 a12 += -nu*v; 01084 a22 += v; 01085 01086 // Contributions from posteriors. 01087 // Skip over any posteriors not yet available 01088 unsigned nspouses =nspouse(); 01089 for (j=0; j<nspouses; j++){ 01090 if (mix_posterior[j].done) { 01091 v = mix_posterior[j].postvec[i_q][i_sw].tsq; 01092 nu = mix_posterior[j].postvec[i_q][i_sw].nu; 01093 k += mix_posterior[j].postvec[i_q][i_sw].k; 01094 a11 += nu*nu*v; 01095 a12 += -nu*v; 01096 a22 += v; 01097 } 01098 } 01099 01100 // compute "log likelihood for gi" 01101 01102 v = 1.0/a22; 01103 g_weight[i_q][i_sw] = -0.5*(a11 - a12*a12*v) 01104 + k + std::log(std::sqrt(4.0*std::asin(1.0)*v)); // pi = 2.0*std::asin(1.0) 01105 sum1 += g_weight[i_q][i_sw]; 01106 } 01107 } 01108 01109 // compute sum of the "likelihoods" 01110 01111 sum1 /= (tng*i_switches); 01112 for (i_q=0;i_q<tng;i_q++){ 01113 sum2=0.0; 01114 for (i_sw=0; i_sw < i_switches; i_sw++){ // loop for genotypes of I 01115 gprobs[i_q] += (std::exp(g_weight[i_q][i_sw] - sum1)); 01116 } 01117 sum2 += gprobs[i_q]; 01118 } 01119 for (i_q=0;i_q<tng;i_q++){ 01120 gprobs[i_q] /= sum2; 01121 } 01122 }

double matvec::Individual::calc_q ( void )

method to calc q prob for individual; q is stored in 1 variable

Definition at line 1293 of file individual.cpp.
References m_gamete, numLoci, p_gamete, population, q_prob, matvec::Population::RecoVector, and matvec::Vector< unsigned >::size().
Referenced by matvec::Population::calc_log_q_ratio(), and put_gametes().

01293 { 01294 // Authors: Matthias Schelling and Rohan L. Fernando 01295 // (1999) 01296 // Contributors: L. Radu Totir 01297 if ((m_gamete.size() == 0) || (p_gamete.size() == 0)) { 01298 throw exception ("Individual::calc_q: no graph present."); 01299 } 01300 double old_q_prob = q_prob; //store old q 01301 if (mymother) { // if not founder 01302 q_prob = 0.25; 01303 for (int j=0; j<numLoci; j++) { 01304 if (m_gamete[j] == m_gamete[j+1]) { 01305 q_prob *= 1 - population->RecoVector[j]; 01306 } 01307 else { 01308 q_prob *= population->RecoVector[j]; 01309 } 01310 if (p_gamete[j] == p_gamete[j+1]) { 01311 q_prob *= 1 - population->RecoVector[j]; 01312 } 01313 else { 01314 q_prob *= population->RecoVector[j]; 01315 } 01316 } 01317 } 01318 else { 01319 q_prob = 1.0; 01320 } 01321 return std::log(old_q_prob) - std::log(q_prob); 01322 }

void matvec::Individual::collapse_antpost ( void )

Definition at line 925 of file individual.cpp.
References anterior, matvec::Dblock::get_ndim(), initial_posterior(), m_anterior, m_posterior, n_switches(), numspouse, posterior, and matvec::Vector< double >::resize().
Referenced by matvec::Population::maxant_maxpost().

00925 { 00926 int i,j, k, nswitch,ndim; 00927 double sum=0.0; 00928 anterior.resize(4,0.0); 00929 initial_posterior(3,-1); 00930 nswitch=n_switches(); 00931 ndim=m_anterior.get_ndim(); 00932 // std::cout << nswitch << m_anterior << anterior << std::endl; 00933 for (k=0; k<ndim; k++) { 00934 for (i=0;i<nswitch;i++){ 00935 // std::cout << i << " " << nswitch << " " << (m_anterior[i][0]) << " " << anterior[i] << std::endl; 00936 anterior[0] += m_anterior[k][i][0]; 00937 anterior[1] += m_anterior[k][i][1] + m_anterior[k][i][2]; 00938 anterior[2] += m_anterior[k][i][3]; 00939 for (j=0;j<numspouse;j++){ 00940 (posterior[j])[0] += (m_posterior[j])[k][i][0]; 00941 (posterior[j])[1] += (m_posterior[j])[k][i][1] + (m_posterior[j])[k][i][2]; 00942 (posterior[j])[2] += (m_posterior[j])[k][i][3]; 00943 } 00944 } 00945 } 00946 }

void matvec::Individual::collapse_mix_antpost ( void )

Definition at line 1124 of file individual.cpp.
References anterior, matvec::DataNode::double_val(), g_weight, gprobs, initial_posterior(), matvec::Population::mean_for_genotype, matvec::DataNode::missing, mix_anterior, mix_posterior, n_switches(), nspouse(), population, posterior, record(), residual_var, and matvec::Vector< double >::resize().
Referenced by matvec::Population::maxant_maxpost().

01124 { 01125 int tng=4; 01126 anterior.resize(tng,0.0); 01127 initial_posterior(tng,-1); 01128 double val,y,v_y,k_y,nu_y, a11, a12, a22, k, v, nu, inverse_sqrt2pi, sum1, sum2; 01129 int i_q, i_sw, i_sp, i_switches,j; 01130 i_switches=n_switches(); 01131 inverse_sqrt2pi = 1.0/std::sqrt(4.0*std::asin(1.0)); // pi = 2.0*std::asin(1.0) 01132 gprobs.resize(3); 01133 val = 0.0; 01134 sum1=0.0; 01135 for (i_q=0;i_q<tng;i_q++){ 01136 // contributions from penetrance function, skip if phenotype is missing 01137 if (!(record()[0].missing)) { 01138 y = record()[0].double_val(); 01139 v_y = 1.0/(*residual_var[0][0]); 01140 k_y = std::log(inverse_sqrt2pi*std::sqrt(v_y)); 01141 nu_y = population->mean_for_genotype[i_q] - y; 01142 } 01143 else{ 01144 nu_y = 0.0; 01145 v_y = 0.0; 01146 k_y = 0.0; 01147 } 01148 01149 for (i_sw=0; i_sw < i_switches; i_sw++){ // loop for genotypes of J 01150 01151 a11 = nu_y*nu_y*v_y; 01152 a12 = nu_y*v_y; 01153 a22 = v_y; 01154 k = k_y; 01155 // contributions from Father's anterior 01156 01157 v = mix_anterior[i_q][i_sw].tsq; 01158 nu = mix_anterior[i_q][i_sw].nu; 01159 k += mix_anterior[i_q][i_sw].k; 01160 a11 += nu*nu*v; 01161 a12 += -nu*v; 01162 a22 += v; 01163 01164 // compute "log likelihood for gi" 01165 v = 1.0/a22; 01166 g_weight[i_q][i_sw] = -0.5*(a11 - a12*a12*v) 01167 + k + std::log(std::sqrt(4.0*std::asin(1.0)*v)); // pi = 2.0*std::asin(1.0) 01168 sum1 += g_weight[i_q][i_sw]; 01169 } 01170 } 01171 01172 // compute sum of the "likelihoods" 01173 01174 sum1 /= (tng*i_switches); 01175 for (i_q=0;i_q<tng;i_q++){ 01176 sum2=0.0; 01177 for (i_sw=0; i_sw < i_switches; i_sw++){ // loop for genotypes of I 01178 anterior[i_q] += (std::exp(g_weight[i_q][i_sw] - sum1)); 01179 } 01180 sum2 += anterior[i_q]; 01181 } 01182 anterior[0] /= sum2; 01183 anterior[1] /= sum2; 01184 anterior[2] /= sum2; 01185 anterior[3] /= sum2; 01186 anterior[1] += anterior[2]; 01187 anterior[2]= anterior[3]; 01188 01189 // Now do the posteriors: 01190 unsigned nspouses =nspouse(); 01191 for (j=0; j<nspouses; j++){ 01192 sum1=0.0; 01193 for (i_q=0;i_q<tng;i_q++){ 01194 for (i_sw=0; i_sw < i_switches; i_sw++){ // loop for genotypes of J 01195 // Contributions from posteriors 01196 01197 if (mix_posterior[j].done) { 01198 v = mix_posterior[j].postvec[i_q][i_sw].tsq; 01199 nu = mix_posterior[j].postvec[i_q][i_sw].nu; 01200 k += mix_posterior[j].postvec[i_q][i_sw].k; 01201 a11 += nu*nu*v; 01202 a12 += -nu*v; 01203 a22 += v; 01204 } 01205 // compute "log likelihood for gi" 01206 v = 1.0/a22; 01207 g_weight[i_q][i_sw] = -0.5*(a11 - a12*a12*v) 01208 + k + std::log(std::sqrt(4.0*std::asin(1.0)*v)); // pi = 2.0*std::asin(1.0) 01209 sum1 += g_weight[i_q][i_sw]; 01210 } 01211 } 01212 01213 // compute sum of the "likelihoods" 01214 01215 sum1 /= (tng*i_switches); 01216 for (i_q=0;i_q<tng;i_q++){ 01217 sum2=0.0; 01218 for (i_sw=0; i_sw < i_switches; i_sw++){ // loop for genotypes of I 01219 posterior[j][i_q] += (std::exp(g_weight[i_q][i_sw] - sum1)); 01220 } 01221 sum2 += posterior[j][i_q]; 01222 } 01223 posterior[j][0] /= sum2; 01224 posterior[j][1] /= sum2; 01225 posterior[j][2] /= sum2; 01226 posterior[j][3] /= sum2; 01227 posterior[j][1] +=posterior[j][2]; 01228 posterior[j][2]=posterior[j][3]; 01229 } 01230 }

void matvec::Individual::copyfrom ( const Individual & A ) [protected]

Definition at line 159 of file individual.cpp.
References anterior, assigned_founder_allele, bet_sw, connect_keeper, eps_sw, est_GV, family, genome0, genome1, genotype_counter, genotype_id, gprobs, group_id, inbc, index_sw, loop_connector, m_anterior, m_anterior_scale, m_posterior, m_posterior_scale, marker_index, MBV, myfather, myid, mymother, myoffspring, myrecord, mysex, numchrom, numoffs, numoffs_spouse, numspouse, numtrait, offs_tree, p_origin, population, posterior, RBV, related_family, residual_var, spouselist, true_GV, and xbzu_val.
Referenced by Individual(), and operator=().

00160 { 00161 if (this == &A) return; 00162 population = A.population; 00163 genotype_id = A.genotype_id; 00164 myid = A.myid; 00165 mysex = A.mysex; inbc = A.inbc; 00166 myfather = A.myfather; mymother = A.mymother; 00167 MBV = A.MBV; RBV = A.RBV; 00168 true_GV = A.true_GV; est_GV = A.est_GV; 00169 xbzu_val = A.xbzu_val; numtrait = A.numtrait; 00170 numspouse = A.numspouse; numoffs = A.numoffs; 00171 group_id = A.group_id; offs_tree = A.offs_tree; 00172 p_origin = A.p_origin; numchrom = A.numchrom; 00173 genome0 = A.genome0; genome1 = A.genome1; 00174 loop_connector = A.loop_connector; anterior = A.anterior; 00175 residual_var = A.residual_var; related_family = A.related_family; 00176 offs_tree = A.offs_tree; connect_keeper = A.connect_keeper; 00177 marker_index = A.marker_index; 00178 assigned_founder_allele = A.assigned_founder_allele; 00179 //BRS 00180 index_sw=A.index_sw; 00181 bet_sw=A.bet_sw; 00182 eps_sw=A.eps_sw; 00183 family=A.family; 00184 gprobs=A.gprobs; 00185 m_anterior=A.m_anterior; 00186 m_posterior=A.m_posterior; 00187 m_anterior_scale=A.m_anterior_scale; 00188 m_posterior_scale=A.m_posterior_scale; 00189 //BRS 00190 00191 unsigned i; 00192 if (posterior) { delete [] posterior; posterior=0;} 00193 if (A.posterior) { 00194 if (numspouse>0){ 00195 posterior = new Vector<double> [numspouse]; 00196 } 00197 else { 00198 posterior = 0; 00199 } 00200 for (i=0; i<numspouse; i++) posterior[i] = A.posterior[i]; 00201 } 00202 if (myrecord) {delete [] myrecord; myrecord = 0;} 00203 if (A.myrecord) { 00204 if(numtrait>0){ 00205 myrecord = new DataNode [numtrait]; 00206 } 00207 else { 00208 myrecord = 0; 00209 } 00210 for (i=0; i<numtrait; i++) myrecord[i] = A.myrecord[i]; 00211 } 00212 if (spouselist) {delete [] spouselist; spouselist= 0;} 00213 if (A.spouselist) { 00214 if (numspouse>0){ 00215 spouselist = new Individual* [numspouse]; 00216 } 00217 else { 00218 spouselist = 0; 00219 } 00220 for (i=0; i<numspouse; i++) spouselist[i] = A.spouselist[i]; 00221 } 00222 if (myoffspring) {delete [] myoffspring; myoffspring=0;} 00223 if (A.myoffspring) { 00224 if(numoffs>0){ 00225 myoffspring = new Individual* [numoffs]; 00226 } 00227 else { 00228 myoffspring = 0; 00229 } 00230 for (i=0; i<numoffs; i++) myoffspring[i] = A.myoffspring[i]; 00231 } 00232 if (numoffs_spouse) { 00233 delete [] numoffs_spouse; numoffs_spouse = 0; 00234 } 00235 if (A.numoffs_spouse) { 00236 if(numspouse>0){ 00237 numoffs_spouse = new unsigned [numspouse]; 00238 } 00239 else { 00240 numoffs_spouse = 0; 00241 } 00242 for (i=0; i<numspouse; i++) numoffs_spouse[i] = A.numoffs_spouse[i]; 00243 } 00244 if (A.genotype_counter) { 00245 if(numchrom>0){ 00246 genotype_counter = new Vector<double> [numchrom]; 00247 } 00248 else { 00249 genotype_counter = 0; 00250 } 00251 for (i=0; i<numchrom; i++) genotype_counter[i] = A.genotype_counter[i]; 00252 } 00253 else { 00254 genotype_counter = 0; 00255 } 00256 }

void matvec::Individual::count_haplotype ( void )

Definition at line 1783 of file individual.cpp.
References matvec::Matrix< unsigned >::empty(), m_gamete, m_haplotype, mymother, numLoci, p_gamete, p_haplotype, and matvec::Matrix< unsigned >::resize().

01783 { 01784 // Authors: Fabiano V. Pita and Rohan L. Fernando 01785 // (2003) 01786 // Contributors: L. Radu Totir 01787 if (m_haplotype.empty()){ 01788 int zero = 0; 01789 m_haplotype.resize(4,numLoci-1,zero); 01790 p_haplotype.resize(4,numLoci-1,zero); 01791 } 01792 01793 if (mymother == NULL) { // if founder 01794 for (int j=1; j<=numLoci-1;j++){ 01795 m_haplotype(1,j) = 0; 01796 m_haplotype(2,j) = 0; 01797 m_haplotype(3,j) = 0; 01798 m_haplotype(4,j) = 0; 01799 p_haplotype(1,j) = 0; 01800 p_haplotype(2,j) = 0; 01801 p_haplotype(3,j) = 0; 01802 p_haplotype(4,j) = 0; 01803 } 01804 } 01805 else { 01806 for (int j=2; j<=numLoci; j++) { 01807 if ((m_gamete(j-1) == 0) && (m_gamete(j) == 0)) { 01808 m_haplotype(1,j-1)+=1; 01809 } 01810 if ((m_gamete(j-1) == 0) && (m_gamete(j) == 1)) { 01811 m_haplotype(2,j-1)+=1; 01812 } 01813 if ((m_gamete(j-1) == 1) && (m_gamete(j) == 0)) { 01814 m_haplotype(3,j-1)+=1; 01815 } 01816 if ((m_gamete(j-1) == 1) && (m_gamete(j) == 1)) { 01817 m_haplotype(4,j-1)+=1; 01818 } 01819 if ((p_gamete(j-1) == 0) && (p_gamete(j) == 0)) { 01820 p_haplotype(1,j-1)+=1; 01821 } 01822 if ((p_gamete(j-1) == 0) && (p_gamete(j) == 1)) { 01823 p_haplotype(2,j-1)+=1; 01824 } 01825 if ((p_gamete(j-1) == 1) && (p_gamete(j) == 0)) { 01826 p_haplotype(3,j-1)+=1; 01827 } 01828 if ((p_gamete(j-1) == 1) && (p_gamete(j) == 1)) { 01829 p_haplotype(4,j-1)+=1; 01830 } 01831 } 01832 } 01833 }

void matvec::Individual::display ( void ) [inline]

Definition at line 166 of file individual.h.
References save().
Referenced by get_penetrance().

00166 {save(std::cout);}

void matvec::Individual::display_freq_haplotype ( unsigned )

Definition at line 1836 of file individual.cpp.
References m_haplotype, myid, numLoci, and p_haplotype.
Referenced by matvec::Model::DGSampler().

01837 { 01838 // Authors: Helene Gilbert and Rohan L. Fernando 01839 // (2004) 01840 // Contributors: L. Radu Totir 01841 double doublen = n; 01842 cout << myid << std::setw(8); 01843 for (int j=1; j<numLoci; j++) { 01844 double m_haplo1 = m_haplotype(1,j); 01845 double m_haplo2 = m_haplotype(2,j); 01846 double m_haplo3 = m_haplotype(3,j); 01847 double m_haplo4 = m_haplotype(4,j); 01848 double p_haplo1 = p_haplotype(1,j); 01849 double p_haplo2 = p_haplotype(2,j); 01850 double p_haplo3 = p_haplotype(3,j); 01851 double p_haplo4 = p_haplotype(4,j); 01852 cout <<m_haplo1/doublen<<" "<<m_haplo2/doublen<<" "<<m_haplo3/doublen<<" "<<m_haplo4/doublen<<" " 01853 <<p_haplo1/doublen<<" "<<p_haplo2/doublen<<" "<<p_haplo3/doublen<<" "<<p_haplo4/doublen<<" "; 01854 } 01855 cout<<endl; 01856 }

void matvec::Individual::displayAlleleVectors ( unsigned locus )

void matvec::Individual::displayGenotypes ( unsigned locus )

unsigned matvec::Individual::family_id ( void ) [inline]

Definition at line 183 of file individual.h.
References group_id.

00183 {return group_id;}

unsigned matvec::Individual::father_gid ( void ) const

Definition at line 319 of file individual.cpp.
References group_id, and myfather.
Referenced by matvec::Population::renum().

00320 { 00321 if (myfather) return myfather->group_id; 00322 else return 0; 00323 }

double matvec::Individual::father_inbcoef ( void ) const

Definition at line 331 of file individual.cpp.
References inbcoef(), and myfather.
Referenced by matvec::Model::add_Ag(), matvec::GLMM::add_Ag(), matvec::Model::add_Ag_diag(), matvec::GLMM::add_Ag_old(), matvec::GLMM::add_AgSand(), matvec::Model::add_G_1_single_trait(), matvec::Population::add_Ga_inv(), matvec::GLMM::ainv(), and matvec::Population::inbcoef_quaas().

00332 { 00333 if (myfather) return myfather->inbcoef(); 00334 else return -1.0; 00335 }

int matvec::Individual::findLeftLocus ( Vector< unsigned > & gamete )

Referenced by matvec::Population::sampleSegregationIndicators().

int matvec::Individual::findRightLocus ( Vector< unsigned > & gamete )

Referenced by matvec::Population::sampleSegregationIndicators().

void matvec::Individual::gamete ( Chromosome * C,

const int n,

const double r

) const

Definition at line 478 of file individual.cpp.
References matvec::Genome::chromosome, genome0, genome1, and numchrom.
Referenced by sample_haplotypes().

00479 { 00480 /************************************************ 00481 * C is non marked genome, D is marked chromosome 00482 ****************************************************/ 00483 if (numchrom != n) throw exception("Individual::gamete(): bad arg"); 00484 const Chromosome *A1, *A2; 00485 A1 = genome0.chromosome; 00486 A2 = genome1.chromosome; 00487 for (unsigned i=0; i<numchrom; i++) { 00488 /* 00489 if (ranf() <= 0.5) { 00490 C[i].qtl = A1[i].qtl; 00491 if (ranf() <= r) { 00492 C[i].marker = A2[i].marker; 00493 } 00494 else { 00495 C[i].marker = A1[i].marker; 00496 } 00497 } 00498 else { 00499 C[i].qtl = A2[i].qtl; 00500 if (ranf() <= r) { 00501 C[i].marker = A1[i].marker; 00502 } 00503 else { 00504 C[i].marker = A2[i].marker; 00505 } 00506 } 00507 */ 00508 } 00509 }

void matvec::Individual::genotype ( const unsigned c,

const unsigned l,

unsigned gtype[]

) const

Definition at line 571 of file individual.cpp.
Referenced by matvec::Population::compute_pdm(), and matvec::Population::llhood_genotype().

00573 { 00574 gtype[0] = genome0.chromosome[c].locus[l].allele; 00575 gtype[1] = genome1.chromosome[c].locus[l].allele; 00576 }

double matvec::Individual::genotypic_val ( void ) const

Definition at line 525 of file individual.cpp.
References genotype_id, matvec::Population::mean_for_genotype, population, and matvec::warning().

00526 { 00527 ///////////////////////////////////////////////////////////////////// 00528 // assuming there are two alleles [0, 1], 00529 // then there are a total of 4 genotypes 00530 // ---------------------- 00531 // | 0 1 00532 // ----------------------- 00533 // 0 | (0 0) (0 1) 00534 // 1 | (1 0) (1 1) 00535 // ------------------------ 00536 // allele id must be an integer starting from 0 00537 /////////////////////////////////////////////////////////////////////// 00538 double retval = 0; 00539 if (genotype_id >= 0) { 00540 retval = population->mean_for_genotype[genotype_id]; 00541 } 00542 else { 00543 warning("Individual::genotypic_val(): no genotype available"); 00544 } 00545 return retval; 00546 /* 00547 unsigned i,j,nc, nl,sd[2]; 00548 nc = prior->nchrom(); 00549 ChromStruct *Chrom = prior->chrom(); 00550 const double** gv; 00551 double retval = 0; 00552 for (i=0; i<nc; i++) { 00553 nl = Chrom[i].nloci(); 00554 for (j=0; j<nl; j++) { 00555 genotype(i,j,sd); 00556 gv = prior->genotypic_val(i,j); 00557 retval += gv[sd[0]][sd[1]]; 00558 } 00559 } 00560 return retval; 00561 */ 00562 }

void matvec::Individual::get_allele_v1 ( unsigned lcs,

Vector< int > allele_vector1

)

Definition at line 1774 of file individual.cpp.
References id(), initial_order1, initial_order2, m_founder, ord_heter, and p_founder.
Referenced by matvec::Population::calc_prior_descent_graph().

01774 { 01775 if (ord_heter == lcs){ 01776 initial_order1 = allele_vector1(m_founder(lcs)); 01777 initial_order2 = allele_vector1(p_founder(lcs)); 01778 std::cout<< id() <<" "<<lcs<<" "<<initial_order1<<" "<<initial_order2<< std::endl; 01779 } 01780 }

int matvec::Individual::get_family ( void ) [inline]

Definition at line 228 of file individual.h.
References family.

00228 {return family;}

Vector< unsigned > & matvec::Individual::get_founder ( std::string ,

bool

)

Definition at line 1426 of file individual.cpp.
References m_founder, p_founder, and set_founder_alleles().
Referenced by set_founder_alleles().

01426 { 01427 set_founder_alleles(update); 01428 01429 if (parent == "mother") { 01430 return m_founder; 01431 } 01432 else { 01433 return p_founder; 01434 } 01435 }

Vector<double> matvec::Individual::get_gprobs ( void ) [inline]

Definition at line 230 of file individual.h.
Referenced by matvec::Population::multi_geno_dist_peeling(), and matvec::Population::multi_m_geno_dist_peeling().

00230 {return gprobs;}

Vector< unsigned > matvec::Individual::get_id_pdq ( void )

Definition at line 1699 of file individual.cpp.
References id_pdq.

01699 { 01700 // Authors: Fabiano V. Pita and Rohan L. Fernando 01701 // (2003) 01702 // Contributors: 01703 return id_pdq; 01704 }

double matvec::Individual::get_m_penetrance ( doubleMatrix & pen )

Definition at line 802 of file individual.cpp.
References matvec::DataNode::double_val(), id(), matvec::Population::mean_for_genotype, matvec::Population::mean_for_pgenotype, matvec::DataNode::missing, myrecord, matvec::Population::P_ndim, population, record(), residual_var, matvec::Matrix< double >::sum(), and matvec::warning().
Referenced by initial_multi_anterior(), matvec::Population::maxant_maxpost(), matvec::NuFamily::multi_anterior(), and matvec::NuFamily::multi_fullsibs_prob().

00802 { 00803 00804 unsigned QTL,PGN; 00805 00806 if (myrecord[0].missing) { 00807 for (PGN=0; PGN<population->P_ndim; PGN++) { 00808 for (QTL=0; QTL<4; QTL++) { 00809 pen[PGN][QTL] = 1.0; 00810 } 00811 } 00812 return 0.0; 00813 } 00814 00815 double inverse_sqrt2pi = 1.0/std::sqrt(4.0*std::asin(1.0)); // pi = 2.0*std::asin(1.0) 00816 double mu, v = *residual_var[0][0],scale; 00817 double y = record()[0].double_val(); 00818 00819 for (PGN=0; PGN<population->P_ndim; PGN++) { 00820 for (QTL=0; QTL<4; QTL++) { 00821 mu = population->mean_for_genotype[QTL]+population->mean_for_pgenotype[PGN]; 00822 pen[PGN][QTL] = inverse_sqrt2pi/std::sqrt(v) * std::exp(-(y-mu)*(y-mu)/(2*v)); 00823 // std::cout << QTL << " Q_mu " << population->mean_for_genotype[QTL] << " P_mu " << population->mean_for_pgenotype[PGN] <<" mu " << mu << " y " << y << " v " << v << " pen is " << setprecision(12) << pen[PGN][QTL] << std::endl; 00824 } 00825 } 00826 // std::cout << "pen in get_m_pen " << pen; 00827 scale = (pen.sum()).sum(); 00828 // std::cout << "Pen scale " << scale << std::endl; 00829 if (fabs(scale) < 1.0e-8) { 00830 std::cout << id() << " has record " << y << std::endl; 00831 warning("this record is not conformable"); 00832 scale = 3.0; 00833 for (PGN=0; PGN<population->P_ndim; PGN++) { 00834 for (QTL=0; QTL<4; QTL++) 00835 pen[PGN][QTL] = 1.0; 00836 } 00837 } 00838 else { 00839 for (PGN=0; PGN<population->P_ndim; PGN++) { 00840 for (QTL=0; QTL<4; QTL++) { 00841 pen[PGN][QTL] /= scale; 00842 } 00843 } 00844 // std::cout << "pen in get pen " << pen << std::endl; 00845 } 00846 return std::log(scale); 00847 }

double matvec::Individual::get_m_posterior ( int excJ,

Dblock & post_mat

)

Definition at line 876 of file individual.cpp.
References matvec::Dblock::get_ndim(), m_posterior, m_posterior_scale, n_switches(), and numspouse.
Referenced by cal_gprobs().

00876 { 00877 00878 ///////////////////////////////////////////////////////// 00879 // if excJ < 0, say -1, means taking all posteriors 00880 ///////////////////////////////////////////////////////// 00881 00882 // make sure post_mat is initialized properly !!!!!!!!!!!!!!!! 00883 00884 unsigned nswitches = n_switches(); 00885 int spouse,i,j,k,ndim; 00886 double retval=0.0; 00887 ndim=post_mat.get_ndim(); 00888 00889 for (spouse=0; spouse<numspouse; spouse++) { 00890 if (spouse != excJ) { 00891 for (k=0; k < ndim; k++){ 00892 for (i=0;i<nswitches; i++){ 00893 for (j=0;j<4;j++){ 00894 post_mat[k][i][j] *= (m_posterior[spouse])[k][i][j]; 00895 } 00896 } 00897 } 00898 retval += m_posterior_scale[spouse]; 00899 } 00900 } 00901 return retval; 00902 }

double matvec::Individual::get_mix_penetrance ( Vector< double > & pen )

Definition at line 1233 of file individual.cpp.
References matvec::DataNode::double_val(), matvec::Population::mean_for_genotype, matvec::DataNode::missing, myrecord, population, record(), residual_var, and matvec::warning().
Referenced by matvec::Population::maxant_maxpost().

01233 { 01234 01235 unsigned QTL,PGN; 01236 01237 if (myrecord[0].missing) { 01238 for (QTL=0; QTL<3; QTL++) { 01239 pen[QTL] = 1.0; 01240 } 01241 return 0.0; 01242 } 01243 01244 double inverse_sqrt2pi = 1.0/std::sqrt(4.0*std::asin(1.0)); // pi = 2.0*std::asin(1.0) 01245 double mu, v = *residual_var[0][0],scale; 01246 double y = record()[0].double_val(); 01247 01248 mu = population->mean_for_genotype[0]; 01249 pen[0] = inverse_sqrt2pi/std::sqrt(v) * std::exp(-(y-mu)*(y-mu)/(2*v)); 01250 mu = population->mean_for_genotype[1]; 01251 pen[1] = inverse_sqrt2pi/std::sqrt(v) * std::exp(-(y-mu)*(y-mu)/(2*v)); 01252 mu = population->mean_for_genotype[2]; 01253 pen[1] += inverse_sqrt2pi/std::sqrt(v) * std::exp(-(y-mu)*(y-mu)/(2*v)); 01254 mu = population->mean_for_genotype[3]; 01255 pen[2] = inverse_sqrt2pi/std::sqrt(v) * std::exp(-(y-mu)*(y-mu)/(2*v)); 01256 01257 scale = pen[0]+ pen[1] + pen[2]; 01258 01259 if (fabs(scale) < 1.0e-8) { 01260 warning("this record is not conformable"); 01261 scale = 3.0; 01262 for (QTL=0; QTL<3; QTL++) 01263 pen[QTL] = 1.0; 01264 } 01265 else { 01266 for (QTL=0; QTL<3; QTL++) { 01267 pen[QTL] /= scale; 01268 } 01269 // std::cout << "pen in get pen " << pen << std::endl; 01270 } 01271 return std::log(scale); 01272 }

double matvec::Individual::get_penetrance ( Vector< double > & pen )

Definition at line 423 of file individual.cpp.
References matvec::Matrix< double >::begin(), display(), matvec::DataNode::double_val(), genotype_id, matvec::Population::mean_for_genotype, matvec::DataNode::missing, myrecord, population, record(), residual_var, matvec::Vector< T >::size(), matvec::Vector< T >::sum(), and matvec::warning().
Referenced by matvec::Population::anterior(), matvec::NuFamily::anterior(), matvec::Population::fullsibs_prob(), matvec::NuFamily::fullsibs_prob(), initial_anterior(), matvec::Population::maxant_maxpost(), and matvec::Population::maxant_maxpost_old().

00424 { 00425 //////////////////////////////////////////////////////////////// 00426 // pen should have enough space to hold all penetrance values 00427 // this works for multi-chromosomes, but not for multi-loci. 00428 // For two chromosomes with two alleles each, there are 10 genotypes 00429 // AB Ab aB ab 00430 // AB 0 00431 // Ab 1 2 00432 // aB 3 4 5 00433 // ab 6 7 8 9 00434 //////////////////////////////////////////////////////////////// 00435 unsigned i,j,t; 00436 unsigned tn_genotype = pen.size(); 00437 if (myrecord[0].missing) { 00438 for (i=0; i<tn_genotype; i++) pen[i] = 1.0; 00439 return 0.0; 00440 } 00441 00442 //* 00443 00444 unsigned tn_gamete = static_cast<unsigned>(0.5*std::sqrt(static_cast<double>(8*tn_genotype + 1)) - 0.5); 00445 for (genotype_id=0,i=0; i<tn_gamete; i++) { 00446 for (j=0; j<=i; j++) { 00447 pen[genotype_id] = (*penetrance_f)(this,(const double**)residual_var->begin()); 00448 genotype_id++; 00449 } 00450 } 00451 00452 //RLF 00453 double inverse_sqrt2pi = 1.0/std::sqrt(4.0*std::asin(1.0)); // pi =2.0*std::asin(1.0) 00454 double mu, v = *residual_var[0][0]; 00455 double y = record()[0].double_val(); 00456 00457 for (i=0; i < tn_genotype; i++) { 00458 mu = population->mean_for_genotype[i]; 00459 pen[i] = inverse_sqrt2pi/std::sqrt(v) * std::exp(-(y-mu)*(y-mu)/(2*v)); 00460 00461 } 00462 //RLF 00463 00464 double scale = pen.sum(); 00465 if (fabs(scale) < 1.0e-8) { 00466 warning("this record is not conformable:"); 00467 this->display(); 00468 scale = 3.0; 00469 for (i=0; i<tn_genotype; i++) pen[i] = 1.0; 00470 } 00471 else { 00472 for (i=0; i<tn_genotype; i++) pen[i] /= scale; 00473 } 00474 return std::log(scale); 00475 }

double matvec::Individual::getAlleleMRTransmissionProb ( unsigned forLocus )

Definition at line 2157 of file individual.cpp.
References malleleOriginNodeVector, malleleStateNodeVector, mymother, and palleleStateNodeVector.
Referenced by matvec::RTransmissionSet::getValue().

02157 { 02158 // Authors: L. Radu Totir and Rohan L. Fernando 02159 // (September, 2004) 02160 // Contributors: 02161 unsigned imState = malleleStateNodeVector[forLocus].getMyAlleleState(); 02162 unsigned mmState = mymother->malleleStateNodeVector[forLocus].getMyAlleleState(); 02163 unsigned mpState = mymother->palleleStateNodeVector[forLocus].getMyAlleleState(); 02164 unsigned imOrigin = malleleOriginNodeVector[forLocus].getMyAlleleOrigin(); 02165 //cout << imState << " " << mmState << " " << mpState 02166 // << " " << imOrigin << endl; 02167 if(imOrigin==0){ 02168 if(imState==mmState){ 02169 return 1.0; 02170 } 02171 else { 02172 return 0.0; 02173 } 02174 } 02175 if(imOrigin==1){ 02176 if(imState==mpState){ 02177 return 1.0; 02178 } 02179 else { 02180 return 0.0; 02181 } 02182 } 02183 }

double matvec::Individual::getAlleleMTransmissionProb ( void )

returns the transmission probability of a maternal allele when the allele origin is assumed known. Used when we peel across pedigree and loci jointly.

Definition at line 2109 of file individual.cpp.
References currentLocus, getTransmissionProb(), m_gamete, malleleStateNodeVector, mymother, and palleleStateNodeVector.
Referenced by matvec::TransmissionSet::getValue().

02109 { 02110 // Authors: L. Radu Totir and Rohan L. Fernando 02111 // (June, 2003) 02112 // Contributors: 02113 unsigned im = malleleStateNodeVector[currentLocus].getMyAlleleState(); 02114 // cout << "Maternal allele for individual: " << myid << " is " << im << endl; 02115 unsigned mm = mymother->malleleStateNodeVector[currentLocus].getMyAlleleState(); 02116 unsigned mp = mymother->palleleStateNodeVector[currentLocus].getMyAlleleState(); 02117 return getTransmissionProb(im,mm,mp,m_gamete); 02118 }

double matvec::Individual::getAllelePenetrance ( unsigned forLocus )

Definition at line 1966 of file individual.cpp.
References matvec::Locus::allele, matvec::GeneticDist::chrom(), matvec::Genome::chromosome, matvec::DataNode::double_val(), genome0, genome1, isqrt2pi, matvec::Chromosome::locus, matvec::ChromStruct::locus, malleleStateNodeVector, matvec::DataNode::missing, myrecord, nQTL, palleleStateNodeVector, population, matvec::Population::prior, QTLPosVector, record(), and residual_var.

01967 { 01968 // Authors: L. Radu Totir and Rohan L. Fernando 01969 // (September, 2004) 01970 // Contributors: 01971 unsigned mState, pState; 01972 if(population->prior->chrom()[0].locus[forLocus].qtl_ml=='q'){ 01973 double mu=0.0,d,pen; 01974 double v = *residual_var[0][0]; 01975 unsigned genoState, QLocus; 01976 if (myrecord[0].missing) { 01977 return 1.0; 01978 } 01979 for (unsigned i=0;i<nQTL;i++) { 01980 QLocus = QTLPosVector[i]; 01981 mState = malleleStateNodeVector[QLocus].getState(); 01982 pState = palleleStateNodeVector[QLocus].getState(); 01983 mu+=population->prior->chrom()[0].locus[QLocus].genotypic_val_mat(pState+1,mState+1); 01984 } 01985 double y = record()[0].double_val(); 01986 pen = isqrt2pi/std::sqrt(v)*std::exp(-(y-mu)*(y-mu)); 01987 return pen; 01988 } 01989 else{ 01990 unsigned allelePat = genome0.chromosome[0].locus[forLocus].allele; 01991 unsigned alleleMat = genome1.chromosome[0].locus[forLocus].allele; 01992 if(allelePat!=0 && allelePat!=alleleMat){ 01993 mState = malleleStateNodeVector[forLocus].getMyAlleleState(); 01994 pState = palleleStateNodeVector[forLocus].getMyAlleleState(); 01995 if(mState != pState){ 01996 return 1.0; 01997 } 01998 else { 01999 return 0.0; 02000 } 02001 } 02002 else { 02003 return 1.0; 02004 } 02005 } 02006 }

double matvec::Individual::getAllelePenetrance ( void )

returns the allele penetrance for the RSampler

Definition at line 1921 of file individual.cpp.
References matvec::GeneticDist::chrom(), matvec::Genome::chromosome, currentLocus, matvec::DataNode::double_val(), genome0, genome1, isqrt2pi, matvec::Chromosome::locus, matvec::ChromStruct::locus, malleleStateNodeVector, matvec::DataNode::missing, myrecord, nQTL, palleleStateNodeVector, population, matvec::Population::prior, QTLPosVector, record(), and residual_var.
Referenced by matvec::RAllelePenetranceSet::getValue(), and matvec::AllelePenetranceSet::getValue().

01922 { 01923 // Authors: L. Radu Totir and Rohan L. Fernando 01924 // (September, 2003) 01925 // Contributors: 01926 unsigned mState, pState; 01927 if(population->prior->chrom()[0].locus[currentLocus].qtl_ml=='q'){ 01928 double mu=0.0,d,pen; 01929 double v = *residual_var[0][0]; 01930 unsigned genoState, QLocus; 01931 if (myrecord[0].missing) { 01932 return 1.0; 01933 } 01934 for (unsigned i=0;i<nQTL;i++) { 01935 QLocus = QTLPosVector[i]; 01936 mState = malleleStateNodeVector[QLocus].getState(); 01937 pState = palleleStateNodeVector[QLocus].getState(); 01938 mu+=population->prior->chrom()[0].locus[QLocus].genotypic_val_mat(pState+1,mState+1); 01939 } 01940 double y = record()[0].double_val(); 01941 pen = isqrt2pi/std::sqrt(v)*std::exp(-(y-mu)*(y-mu)); 01942 return pen; 01943 } 01944 else{ 01945 unsigned allelePat = genome0.chromosome[0].locus[currentLocus].allele; 01946 unsigned alleleMat = genome1.chromosome[0].locus[currentLocus].allele; 01947 if(allelePat!=0 && allelePat!=alleleMat){ 01948 mState = malleleStateNodeVector[currentLocus].getMyAlleleState(); 01949 pState = palleleStateNodeVector[currentLocus].getMyAlleleState(); 01950 if(mState != pState){ 01951 return 1.0; 01952 } 01953 else { 01954 return 0.0; 01955 } 01956 } 01957 else { 01958 return 1.0; 01959 } 01960 } 01961 }

double matvec::Individual::getAllelePRTransmissionProb ( unsigned forLocus )

Definition at line 2124 of file individual.cpp.
References malleleStateNodeVector, myfather, palleleOriginNodeVector, and palleleStateNodeVector.
Referenced by matvec::RTransmissionSet::getValue().

02124 { 02125 // Authors: L. Radu Totir and Rohan L. Fernando 02126 // (September, 2004) 02127 // Contributors: 02128 unsigned ipState = palleleStateNodeVector[forLocus].getMyAlleleState(); 02129 unsigned fmState = myfather->malleleStateNodeVector[forLocus].getMyAlleleState(); 02130 unsigned fpState = myfather->palleleStateNodeVector[forLocus].getMyAlleleState(); 02131 unsigned ipOrigin = palleleOriginNodeVector[forLocus].getMyAlleleOrigin(); 02132 // cout << ipState << " " << fmState << " " << fpState 02133 // << " " << ipOrigin << endl; 02134 if(ipOrigin==0){ 02135 if(ipState==fmState){ 02136 return 1.0; 02137 } 02138 else { 02139 return 0.0; 02140 } 02141 } 02142 if(ipOrigin==1){ 02143 if(ipState==fpState){ 02144 return 1.0; 02145 } 02146 else { 02147 return 0.0; 02148 } 02149 } 02150 }

double matvec::Individual::getAllelePTransmissionProb ( void )

returns the transmission probability of a paternal allele when the allele origin is assumed known. Used when we peel across pedigree and loci jointly.

Definition at line 2093 of file individual.cpp.
References currentLocus, getTransmissionProb(), malleleStateNodeVector, myfather, p_gamete, and palleleStateNodeVector.
Referenced by matvec::TransmissionSet::getValue().

02093 { 02094 // Authors: L. Radu Totir and Rohan L. Fernando 02095 // (June, 2003) 02096 // Contributors: 02097 // cout << currentLocus << endl; 02098 unsigned ip = palleleStateNodeVector[currentLocus].getMyAlleleState(); 02099 unsigned fm = myfather->malleleStateNodeVector[currentLocus].getMyAlleleState(); 02100 unsigned fp = myfather->palleleStateNodeVector[currentLocus].getMyAlleleState(); 02101 // cout << ip << " " << fm << " " << fp << endl; 02102 return getTransmissionProb(ip,fm,fp,p_gamete); 02103 }

double matvec::Individual::getDisAllelePenetrance ( unsigned forLocus )

Definition at line 2030 of file individual.cpp.
References matvec::Population::disPenetranceTable, malleleStateNodeVector, matvec::DataNode::missing, myrecord, palleleStateNodeVector, population, and record().

02031 { 02032 // Authors: L. Radu Totir and Rohan L. Fernando 02033 // (September, 2004) 02034 // Contributors: 02035 double mu=0.0,d,pen; 02036 unsigned mState, pState; 02037 if (myrecord[0].missing) { 02038 return 1.0; 02039 } 02040 mState = malleleStateNodeVector[forLocus].getState(); 02041 pState = palleleStateNodeVector[forLocus].getState(); 02042 int phenotype = int(record()[0].double_val()); 02043 // cout << phenotype << " " << mState+pState << " " 02044 // << population->disPenetranceTable[phenotype][mState+pState] 02045 // << endl; 02046 return population->disPenetranceTable[phenotype][mState+pState]; 02047 }

double matvec::Individual::getDisAllelePenetrance ( void )

Definition at line 2011 of file individual.cpp.
References currentLocus, matvec::Population::disPenetranceTable, malleleStateNodeVector, matvec::DataNode::missing, myrecord, palleleStateNodeVector, population, and record().
Referenced by matvec::RDisAllelePenetranceSet::getValue(), and matvec::DisAllelePenetranceSet::getValue().

02012 { 02013 // Authors: L. Radu Totir and Rohan L. Fernando 02014 // (September, 2004) 02015 // Contributors: 02016 double mu=0.0,d,pen; 02017 unsigned mState, pState; 02018 if (myrecord[0].missing) { 02019 return 1.0; 02020 } 02021 mState = malleleStateNodeVector[currentLocus].getState(); 02022 pState = palleleStateNodeVector[currentLocus].getState(); 02023 int phenotype = int(record()[0].double_val()); 02024 // cout << phenotype << " " << mState+pState << " " 02025 // << population->disPenetranceTable[phenotype][mState+pState] 02026 // << endl; 02027 return population->disPenetranceTable[phenotype][mState+pState]; 02028 }

double matvec::Individual::getDisGenoPenetrance ( void )

Definition at line 2074 of file individual.cpp.
References currentLocus, matvec::Population::disPenetranceTable, genotNodeVector, matvec::DataNode::missing, myrecord, population, and record().
Referenced by matvec::DisGenoPenetranceSet::getValue().

02075 { 02076 // Authors: L. Radu Totir and Rohan L. Fernando 02077 // (August, 2004) 02078 // Contributors: 02079 double mu=0.0,d,pen; 02080 unsigned mState, pState; 02081 if (myrecord[0].missing) { 02082 return 1.0; 02083 } 02084 mState = genotNodeVector[currentLocus].getmState(); 02085 pState = genotNodeVector[currentLocus].getpState(); 02086 int phenotype = int(record()[0].double_val()); 02087 // cout << phenotype << " " << mState+pState << " " 02088 // << population->disPenetranceTable[phenotype][mState+pState] 02089 // << endl; 02090 return population->disPenetranceTable[phenotype][mState+pState]; 02091 }

double matvec::Individual::getGenoPenetrance ( void )

returns the genotype penetrance for the RSampler

Definition at line 2049 of file individual.cpp.
References matvec::GeneticDist::chrom(), matvec::DataNode::double_val(), genotNodeVector, isqrt2pi, matvec::ChromStruct::locus, matvec::DataNode::missing, myrecord, nQTL, population, matvec::Population::prior, QTLPosVector, record(), and residual_var.
Referenced by matvec::GenoPenetranceSet::getValue().

02050 { 02051 // Authors: L. Radu Totir and Rohan L. Fernando 02052 // (June, 2003) 02053 // Contributors: 02054 double mu=0.0,d,pen; 02055 double v = *residual_var[0][0]; 02056 unsigned mState, pState, QLocus; 02057 if (myrecord[0].missing) { 02058 return 1.0; 02059 } 02060 for (unsigned i=0;i<nQTL;i++) { 02061 QLocus = QTLPosVector[i]; 02062 mState = genotNodeVector[QLocus].getmState(); 02063 pState = genotNodeVector[QLocus].getpState(); 02064 mu+=population->prior->chrom()[0].locus[QLocus].genotypic_val_mat(pState+1,mState+1); 02065 } 02066 double y = record()[0].double_val(); 02067 pen = isqrt2pi/std::sqrt(v)*std::exp(-(y-mu)*(y-mu)); 02068 return pen; 02069 }

double matvec::Individual::getMatthiasMTransmissionProb ( void )

double matvec::Individual::getMatthiasPTransmissionProb ( void )

double matvec::Individual::getMatthiasTransitionProb ( void )

Referenced by matvec::TransitionSet::getValue().

double matvec::Individual::getMatthiasTransmissionProb ( unsigned iA,

unsigned mA,

unsigned pA,

Vector< unsigned > & gamete,

Vector< unsigned > & gameteOld

)

double matvec::Individual::getMTransmissionProb ( void )

returns the maternal allele transmission probability for the RSampler for genotype peeling

Definition at line 2217 of file individual.cpp.
References currentLocus, genotNodeVector, getTransmissionProb(), m_gamete, and mymother.
Referenced by getTransitionProb().

02217 { 02218 // Authors: L. Radu Totir and Rohan L. Fernando 02219 // (June, 2003) 02220 // Contributors: 02221 unsigned im = genotNodeVector[currentLocus].getmState(); 02222 unsigned mm = mymother->genotNodeVector[currentLocus].getmState(); 02223 unsigned mp = mymother->genotNodeVector[currentLocus].getpState(); 02224 return getTransmissionProb(im,mm,mp,m_gamete); 02225 }

double matvec::Individual::getPTransmissionProb ( void )

returns the paternal allele transmission probability for the RSampler for genotype peeling

Definition at line 2203 of file individual.cpp.
References currentLocus, genotNodeVector, getTransmissionProb(), myfather, and p_gamete.
Referenced by getTransitionProb().

02203 { 02204 // Authors: L. Radu Totir and Rohan L. Fernando 02205 // (June, 2003) 02206 // Contributors: 02207 unsigned ip = genotNodeVector[currentLocus].getpState(); 02208 unsigned fm = myfather->genotNodeVector[currentLocus].getmState(); 02209 unsigned fp = myfather->genotNodeVector[currentLocus].getpState(); 02210 return getTransmissionProb(ip,fm,fp,p_gamete); 02211 }

double matvec::Individual::getTransitionProb ( void )

returns the genotype transition probability in the RSampler

Definition at line 2190 of file individual.cpp.
References getMTransmissionProb(), and getPTransmissionProb().
Referenced by matvec::TransitionSet::getTargetValue(), and matvec::TransitionSet::getValue().

02190 { 02191 // Authors: L. Radu Totir and Rohan L. Fernando 02192 // (June, 2003) 02193 // Contributors: 02194 double result; 02195 result = getMTransmissionProb()*getPTransmissionProb(); 02196 return result; 02197 }

double matvec::Individual::getTransmissionProb ( unsigned iA,

unsigned mA,

unsigned pA,

Vector< unsigned > & gamete

)

Referenced by getAlleleMTransmissionProb(), getAllelePTransmissionProb(), getMTransmissionProb(), and getPTransmissionProb().

unsigned matvec::Individual::gid ( void ) const [inline]

Definition at line 192 of file individual.h.
References group_id.
Referenced by matvec::NuFamily::build_connectors(), and matvec::Population::renum().

00192 {return group_id;}

double matvec::Individual::graph_trans_prob ( unsigned ,

unsigned ,

unsigned

)

Definition at line 1447 of file individual.cpp.
References matvec::Model::gamete_prob_table, m_gamete, matvec::Population::model, p_gamete, population, and matvec::Vector< unsigned >::size().

01449 { 01450 double m_prob=0, f_prob=0; 01451 unsigned FQTable[4][4]={2,3,2,3,0,1,0,1,1,0,1,0,3,2,3,2}; 01452 unsigned MQTable[4][4]={2,2,3,3,0,0,1,1,1,1,0,0,3,3,2,2}; 01453 unsigned FQindex = FQTable[uf][uj]; 01454 unsigned MQindex = MQTable[um][uj]; 01455 unsigned MMindex = 0, FMindex = 0, size = m_gamete.size(); 01456 01457 //calc marker indexes (bin -> dec) 01458 for(int k = size; k > 0; k--){ 01459 /*std::cout << "m_marker" << k << '\t' << m_gamete(k) 01460 << "\tp_marker" << k << '\t' << p_gamete(k) 01461 << std::endl; 01462 */ 01463 MMindex+=(unsigned)((1 << (size-k)))*m_gamete(k); 01464 FMindex+=(unsigned)((1 << (size-k)))*p_gamete(k); 01465 } 01466 01467 if(FQindex==3 || MQindex==3){return 0.0;} 01468 if(FQindex==2){f_prob=1;} 01469 else{ 01470 f_prob=population->model->gamete_prob_table[FMindex][FQindex]; 01471 //std::cout << "FMindex: " << FMindex << "\tFQindex: " << FQindex << std::endl; 01472 } 01473 if(MQindex==2){m_prob=1;} 01474 else{ 01475 m_prob=population->model->gamete_prob_table[MMindex][MQindex]; 01476 //std::cout << "MMindex: " << MMindex << "\tMQindex: " << MQindex << std::endl; 01477 } 01478 //return transition (transmission*transmission) probability 01479 //std::cerr << "return transition " << f_prob*m_prob << std::endl; 01480 return f_prob*m_prob; 01481 }

double matvec::Individual::inbcoef ( void ) const [inline]

Definition at line 178 of file individual.h.
References inbc.
Referenced by father_inbcoef(), matvec::Population::inbcoef(), and mother_inbcoef().

00178 {return inbc;}

void matvec::Individual::initial_anterior ( const double * gfreq,

const unsigned tng,

const int cond = -1

)

Definition at line 343 of file individual.cpp.
References anterior, anterior_iw, get_penetrance(), matvec::DataNode::missing, myrecord, matvec::Vector< double >::resize(), and matvec::Vector< double >::size().
Referenced by matvec::NuFamily::cutting(), matvec::Population::maxant_maxpost(), matvec::Population::maxant_maxpost_old(), and pretend_missing().

00345 { 00346 ///////////////////////////////////////////////////////////////////////// 00347 // Conditional initialization for anterior 00348 // cond = -1 is the default, means initialize anterior un-conditionally 00349 // cond = 1, associated with extra data resulting from iterating 00350 ///////////////////////////////////////////////////////////////////// 00351 00352 if (cond == anterior_iw) return; // anterior_iw is the condition 00353 unsigned j; 00354 if (anterior.size() != tng+1) anterior.resize(tng+1); 00355 if (myrecord[0].missing) { 00356 for (j=0; j<tng; j++) anterior[j] = gfreq[j]; 00357 anterior[tng] = 0.0; 00358 return; 00359 } 00360 double s; 00361 Vector<double> pen_vec(tng); 00362 anterior[tng] = get_penetrance(pen_vec); 00363 for (s=0.0,j=0; j<tng; j++) s += (anterior[j] = pen_vec[j]*gfreq[j]); 00364 for (j=0; j<tng; j++) anterior[j] /= s; 00365 anterior[tng] += std::log(s); 00366 }

void matvec::Individual::initial_multi_anterior ( doubleMatrix & penetrance )

Definition at line 711 of file individual.cpp.
References matvec::Locus::allele, matvec::Genome::chromosome, genome0, genome1, get_m_penetrance(), matvec::Dblock::get_nrow(), index_sw, matvec::Chromosome::locus, m_anterior, m_anterior_iw, m_anterior_scale, matvec::Population::marker_freq, matvec::DataNode::missing, myrecord, matvec::Population::n_markerLoci, matvec::Population::P_freq, matvec::Population::P_ndim, matvec::penetrance(), population, matvec::Population::Q_freq, matvec::Dblock::resize(), and matvec::Population::switch_table.
Referenced by matvec::NuFamily::cutting(), matvec::Population::maxant_maxpost(), matvec::NuFamily::multi_initialize(), matvec::Population::multipoint_likelihood(), and pretend_multi_missing().

00712 { 00713 unsigned i,j,k,a1,a2,ndim; 00714 double freq, scale, sum=0.0, freq_mark=1.0; 00715 unsigned n_switch = population->switch_table[index_sw][0]; 00716 ndim=population->P_ndim; 00717 if (m_anterior.get_nrow() != n_switch) m_anterior.resize(ndim,n_switch,4,0.0); 00718 m_anterior_iw = 0; 00719 00720 for (k=1;k<=population->n_markerLoci; k++){ 00721 a1 = genome0.chromosome[0].locus[k].allele; 00722 a2 = genome1.chromosome[0].locus[k].allele; 00723 freq_mark *= population->marker_freq(k)(a1)*population->marker_freq(k)(a2); 00724 } 00725 if (myrecord[0].missing) { 00726 m_anterior_scale =0.0; 00727 for (k=0;k<ndim; k++){ 00728 for (j=0; j<4; j++) { 00729 freq = (population->Q_freq[j])*freq_mark*(population->P_freq[k]); 00730 for (i=0; i<n_switch; i++) { 00731 m_anterior[k][i][j] = freq; 00732 sum += freq; // accumulating scaling factor 00733 } 00734 } 00735 } 00736 } 00737 else { 00738 // std::cout << " before call Pen " << std::endl; 00739 m_anterior_scale = get_m_penetrance(penetrance); 00740 // std::cout << "scale in intial_anterior "<< m_anterior_scale << std::endl; 00741 // std::cout << " Pen " << penetrance << std::endl; 00742 for (k=0;k<ndim; k++){ 00743 for (j=0; j<4; j++) { 00744 freq = (population->Q_freq[j])*freq_mark*(population->P_freq[k])*penetrance[k][j]; 00745 // std::cout << "k " << k << " j " << j << " Q_f " << population->Q_freq[j]; 00746 // std::cout << " M_f " << freq_mark << " Pen " << penetrance[k][j] << " freq " << freq << std::endl; 00747 for (i=0; i<n_switch; i++) { 00748 m_anterior[k][i][j] = freq; 00749 sum += freq; // accumulating scaling factor 00750 } 00751 } 00752 } 00753 } 00754 // std::cout << "sum " << sum << std::endl; 00755 00756 // Need to rescale due to probability of observing the marker genotypes 00757 for (k=0;k<ndim; k++){ 00758 for (i=0; i<n_switch; i++) { 00759 for (j=0; j<4; j++) { 00760 m_anterior[k][i][j] /= sum; 00761 } 00762 } 00763 } 00764 m_anterior_scale += std::log(sum); 00765 // std::cout << "scale " << m_anterior_scale << std::endl; 00766 }

void matvec::Individual::initial_multi_m_anterior ( const unsigned tn_qtl )

Definition at line 973 of file individual.cpp.
References matvec::Locus::allele, matvec::Genome::chromosome, matvec::Population::F, genome0, genome1, matvec::Chromosome::locus, matvec::Population::marker_freq, mix_anterior, matvec::Population::n_markerLoci, n_switches(), population, matvec::Population::Q_freq, matvec::Vector< Vector< UNormal > >::resize(), matvec::Vector< Vector< UNormal > >::size(), and matvec::Fpmm::var.
Referenced by matvec::NuFamily::cutting(), matvec::Population::maxant_maxpost(), matvec::Population::multi_m_geno_dist_peeling(), matvec::NuFamily::multi_m_initialize(), and pretend_multi_m_missing().

00973 { 00974 int i_q, i_sw, i_switches,k, a1, a2; 00975 double freq_mark=1.0; 00976 double P_var = population->F->var; // polygenic varaince 00977 i_switches=n_switches(); 00978 00979 // compute frequency of marker information 00980 for (k=1;k<=population->n_markerLoci; k++){ 00981 a1 = genome0.chromosome[0].locus[k].allele; 00982 a2 = genome1.chromosome[0].locus[k].allele; 00983 freq_mark *= population->marker_freq(k)(a1)*population->marker_freq(k)(a2); 00984 } 00985 00986 if (tn_qtl != mix_anterior.size()) 00987 mix_anterior.resize(tn_qtl); 00988 for (i_q=0; i_q < tn_qtl; i_q++){ 00989 mix_anterior[i_q].resize(i_switches); 00990 for (i_sw=0; i_sw < i_switches; i_sw++) { 00991 mix_anterior[i_q][i_sw].nu = 0.0; 00992 mix_anterior[i_q][i_sw].tsq = 1.0/P_var; 00993 mix_anterior[i_q][i_sw].k = std::log(1.0/std::sqrt(4.0*std::asin(1.0)*P_var)*population->Q_freq[i_q]*freq_mark); 00994 // std::cout << id() << " " << i_q << " " << i_sw << " nu " << mix_anterior[i_q][i_sw].nu << " tsq " << mix_anterior[i_q][i_sw].tsq << " k " << mix_anterior[i_q][i_sw].k << std::endl; 00995 } 00996 } 00997 // std::cout << "anterior initialized for " << id() << std::endl; 00998 }

void matvec::Individual::initial_multi_m_posterior ( const unsigned tn_qtl,

const int cond

)

Definition at line 1000 of file individual.cpp.
References mix_posterior, n_switches(), numspouse, posterior_iw, matvec::Vector< double >::resize(), matvec::Vector< Mixed_post_vec >::resize(), and matvec::Vector< Mixed_post_vec >::size().
Referenced by matvec::NuFamily::cutting(), matvec::Population::maxant_maxpost(), matvec::NuFamily::multi_m_initialize(), and pretend_multi_m_missing().

01000 { 01001 01002 int i_q, i_sw,spouse,i_switches, i_s; 01003 i_switches=n_switches(); 01004 if (numspouse) { 01005 if (mix_posterior.size() != numspouse) { 01006 mix_posterior.resize(numspouse); 01007 posterior_iw.resize(numspouse,0.0); 01008 for (spouse=0; spouse<numspouse; spouse++) { 01009 mix_posterior[spouse].done = 0; 01010 mix_posterior[spouse].postvec.resize(tn_qtl); 01011 for (i_q=0; i_q < tn_qtl; i_q++) { 01012 mix_posterior[spouse].postvec[i_q].resize(i_switches); 01013 } 01014 } 01015 } 01016 else { 01017 if (posterior){ 01018 mix_posterior.resize(numspouse); 01019 posterior_iw.resize(numspouse,0.0); 01020 for (spouse=0; spouse<numspouse; spouse++) { 01021 if (posterior_iw[spouse] != cond) { 01022 mix_posterior[spouse].done = 0; 01023 mix_posterior[spouse].postvec.resize(tn_qtl); 01024 for (i_q=0; i_q < tn_qtl; i_q++) { 01025 mix_posterior[spouse].postvec[i_q].resize(i_switches); 01026 } 01027 } 01028 } 01029 } 01030 } 01031 } 01032 else { 01033 mix_posterior.resize(numspouse); 01034 for (spouse=0; spouse < numspouse; spouse++){ 01035 mix_posterior[spouse].done = 0; 01036 mix_posterior[spouse].postvec.resize(tn_qtl); 01037 for (i_q=0; i_q < tn_qtl; i_q++) { 01038 mix_posterior[spouse].postvec[i_q].resize(i_switches); 01039 } 01040 } 01041 } 01042 }

void matvec::Individual::initial_multi_posterior ( const int cond )

Definition at line 768 of file individual.cpp.
References index_sw, m_posterior, m_posterior_scale, numspouse, matvec::Population::P_ndim, population, posterior_iw, matvec::Vector< double >::resize(), matvec::Vector< Dblock >::resize(), matvec::Vector< Dblock >::size(), and matvec::Population::switch_table.
Referenced by matvec::NuFamily::cutting(), matvec::Population::maxant_maxpost(), matvec::Population::multi_geno_dist_peeling(), matvec::NuFamily::multi_initialize(), matvec::Population::multipoint_likelihood(), and pretend_multi_missing().

00768 { 00769 ///////////////////////////////////////////////////////////////////////// 00770 // Conditional initialization for posterior 00771 // cond = -1 is the default, means initialize anterior un-conditionally 00772 // cond = 1, associated with extra data resulting from iterating 00773 ///////////////////////////////////////////////////////////////////// 00774 int i,ndim; 00775 unsigned n_switch = population->switch_table[index_sw][0]; 00776 ndim=population->P_ndim; 00777 if (numspouse) { 00778 if (m_posterior.size() != numspouse ) { 00779 m_posterior.resize(numspouse); 00780 m_posterior_scale.resize(numspouse,0.0); 00781 posterior_iw.resize(numspouse,0.0); //BRS 00782 } 00783 if (posterior){ 00784 m_posterior_scale.resize(numspouse,0.0); 00785 posterior_iw.resize(numspouse,0.0); //BRS 00786 for (i=0; i<numspouse; i++) { 00787 if (posterior_iw[i] != cond) { 00788 m_posterior[i].resize(ndim,n_switch,4,1.0); 00789 } 00790 } 00791 } 00792 else { 00793 for (i=0; i<numspouse; i++) { 00794 m_posterior[i].resize(ndim,n_switch,4,1.0); 00795 } 00796 m_posterior_scale.resize(numspouse,0.0); 00797 posterior_iw.resize(numspouse,0.0); //BRS 00798 } 00799 } 00800 }

void matvec::Individual::initial_posterior ( const unsigned tng,

const int cond = -1

)

Definition at line 368 of file individual.cpp.
References numspouse, posterior, posterior_iw, and matvec::Vector< double >::resize().
Referenced by collapse_antpost(), collapse_mix_antpost(), matvec::NuFamily::cutting(), matvec::Population::maxant_maxpost(), matvec::Population::maxant_maxpost_old(), matvec::Model::multipoint_genot_probs(), and pretend_missing().

00369 { 00370 ///////////////////////////////////////////////////////////////////////// 00371 // Conditional initialization for posterior 00372 // cond = -1 is the default, means initialize anterior un-conditionally 00373 // cond = 1, associated with extra data resulting from iterating 00374 ///////////////////////////////////////////////////////////////////// 00375 int i; 00376 if (posterior) { 00377 for (i=0; i<numspouse; i++) { 00378 if (posterior_iw[i] != cond) { 00379 posterior[i].resize(tng+1,1.0); 00380 posterior[i][tng] = 0.0; 00381 } 00382 } 00383 } 00384 else { 00385 if(numspouse>0){ 00386 posterior = new Vector<double> [numspouse]; 00387 posterior_iw.resize(numspouse,0.0); //BRS 00388 } 00389 else { 00390 posterior = 0; 00391 } 00392 for (i=0; i<numspouse; i++) { 00393 posterior[i].resize(tng+1,1.0); 00394 posterior[i][tng] = 0.0; 00395 } 00396 } 00397 }

int matvec::Individual::isolated ( ) const [inline]

Definition at line 160 of file individual.h.
References numoffs.
Referenced by matvec::Population::mark_relative_recursive(), matvec::Population::multi_m_log_likelihood_peeling(), and matvec::Population::multipoint_likelihood().

00160 {return !(myfather || mymother || numoffs);}

void matvec::Individual::map_pdq ( int samples,

int interval,

BG r_aq,

BG r_bq

)

Definition at line 1863 of file individual.cpp.
References bgDMPDQ, bgSMPDQ, m_haplotype, mymother, and p_haplotype.

01863 { 01864 double doubleSample = samples; 01865 BG r_ab = (1-r_aq)*r_bq + r_aq*(1-r_bq); 01866 if (mymother == NULL) { // if founder 01867 bgDMPDQ = 0.0; 01868 bgSMPDQ = 0.0; 01869 } 01870 else { 01871 // bgDMPDQ = (1-r_aq)*(1-r_bq)*m_haplotype(1,interval)/samples + (1-r_aq)*(r_bq)*m_haplotype(2,interval)/samples 01872 // + (r_aq)*(1-r_bq)*m_haplotype(3,interval)/samples + (r_aq)*(r_bq)*m_haplotype(4,interval)/samples; 01873 01874 // bgSMPDQ = (1-r_aq)*(1-r_bq)*p_haplotype(1,interval)/samples + (1-r_aq)*(r_bq)*p_haplotype(2,interval)/samples 01875 // + (r_aq)*(1-r_bq)*p_haplotype(3,interval)/samples + (r_aq)*(r_bq)*p_haplotype(4,interval)/samples; 01876 // !!! 01877 // bgDMPDQ = m_haplotype(1,interval)/doubleSample + r_bq/(r_aq+r_bq)*m_haplotype(2,interval)/doubleSample 01878 // + (r_aq/(r_aq+r_bq))*m_haplotype(3,interval)/doubleSample ; 01879 01880 // bgSMPDQ = p_haplotype(1,interval)/doubleSample + r_bq/(r_aq+r_bq)*p_haplotype(2,interval)/doubleSample 01881 // + ((r_aq)/(r_aq+r_bq))*p_haplotype(3,interval)/doubleSample; 01882 bgDMPDQ = (1-r_aq)*(1-r_bq) / (1-r_ab) * m_haplotype(1,interval)/doubleSample 01883 + (1-r_aq)*(r_bq) / r_ab * m_haplotype(2,interval)/doubleSample 01884 + (r_aq) *(1-r_bq) / r_ab * m_haplotype(3,interval)/doubleSample 01885 + (r_aq)*(r_bq) / (1-r_ab) * m_haplotype(4,interval)/doubleSample; 01886 01887 bgSMPDQ = (1-r_aq)*(1-r_bq) / (1-r_ab) * p_haplotype(1,interval)/doubleSample 01888 + (1-r_aq)*(r_bq) / r_ab * p_haplotype(2,interval)/doubleSample 01889 + (r_aq) *(1-r_bq) / r_ab * p_haplotype(3,interval)/doubleSample 01890 + (r_aq)*(r_bq) / (1-r_ab) * p_haplotype(4,interval)/doubleSample; 01891 // !!! 01892 // cout<<interval<<" Maternal haplotype pty "<< m_haplotype(1,interval)<<" "<<m_haplotype(2,interval)<<" "<<m_haplotype(3,interval)<<" "<<bgDMPDQ.f<<endl; 01893 // cout<<interval<<" Paternal haplotype pty "<< p_haplotype(1,interval)<<" "<<p_haplotype(2,interval)<<" "<<p_haplotype(3,interval)<<" "<<bgSMPDQ.f<<endl; 01894 } 01895 }

void matvec::Individual::map_pdq ( int samples,

int interval,

double r_aq,

double r_bq

)

unsigned matvec::Individual::marked ( void ) const [inline]

Definition at line 184 of file individual.h.
References group_id.

00184 {return group_id;}

Chromosome* matvec::Individual::maternal_chrom ( void ) [inline]

Definition at line 205 of file individual.h.
References matvec::Genome::chromosome.
Referenced by matvec::Population::cond_genotype_config(), matvec::Population::genotype_config(), matvec::Population::gibbs_iterate(), and matvec::Population::llhood_phenotype().

00205 {return genome1.chromosome;}

unsigned matvec::Individual::maternal_chrom_id ( const unsigned c ) const [inline]

Definition at line 195 of file individual.h.
References matvec::Genome::chromosome, and matvec::Chromosome::id().
Referenced by matvec::Population::count_genotype(), matvec::Population::cprob_children(), and matvec::Population::ind_gamete().

00196 {return genome1.chromosome[c].id();}

unsigned matvec::Individual::mother_gid ( void ) const

Definition at line 325 of file individual.cpp.
References group_id, and mymother.
Referenced by matvec::Population::renum().

00326 { 00327 if (mymother) return mymother->group_id; 00328 else return 0; 00329 }

double matvec::Individual::mother_inbcoef ( void ) const

Definition at line 337 of file individual.cpp.
References inbcoef(), and mymother.
Referenced by matvec::Model::add_Ag(), matvec::GLMM::add_Ag(), matvec::Model::add_Ag_diag(), matvec::GLMM::add_Ag_old(), matvec::GLMM::add_AgSand(), matvec::Model::add_G_1_single_trait(), matvec::Population::add_Ga_inv(), matvec::GLMM::ainv(), and matvec::Population::inbcoef_quaas().

00338 { 00339 if (mymother) return mymother->inbcoef(); 00340 else return -1.0; 00341 }

unsigned matvec::Individual::nchrom ( void ) const [inline]

Definition at line 182 of file individual.h.
References numchrom.

00182 {return numchrom;}

unsigned matvec::Individual::noffs ( void ) const [inline]

Definition at line 188 of file individual.h.
References numoffs.
Referenced by matvec::Population::cprob_children(), matvec::Population::full_cdist(), matvec::Population::mark_descendant_recursive(), and matvec::Population::mark_relative_recursive().

00188 {return numoffs;}

const unsigned* matvec::Individual::noffs_spouse ( void ) const [inline]

Definition at line 189 of file individual.h.
References numoffs_spouse.
Referenced by matvec::Population::build_nufamily(), matvec::Population::fullsibs_prob(), and matvec::Population::partial_iterative_peeling().

00189 {return numoffs_spouse;}

Individual** matvec::Individual::offspring ( void ) const [inline]

Definition at line 208 of file individual.h.
Referenced by matvec::Population::build_nufamily(), matvec::Population::build_spouse_info(), matvec::Population::cprob_children(), matvec::Population::fullsibs_prob(), and matvec::Population::partial_iterative_peeling().

00208 {return myoffspring;}

const Individual & matvec::Individual::operator= ( const Individual & A )

Definition at line 301 of file individual.cpp.
References copyfrom().

00302 { 00303 copyfrom(A); 00304 return *this; 00305 }

void matvec::Individual::parents ( void )

Chromosome* matvec::Individual::paternal_chrom ( void ) [inline]

Definition at line 204 of file individual.h.
References matvec::Genome::chromosome.
Referenced by matvec::Population::cond_genotype_config(), matvec::Population::genotype_config(), matvec::Population::gibbs_iterate(), and matvec::Population::llhood_phenotype().

00204 {return genome0.chromosome;}

unsigned matvec::Individual::paternal_chrom_id ( const unsigned c ) const [inline]

Definition at line 193 of file individual.h.
References matvec::Genome::chromosome, and matvec::Chromosome::id().
Referenced by matvec::Population::count_genotype(), matvec::Population::cprob_children(), and matvec::Population::ind_gamete().

00194 {return genome0.chromosome[c].id();}

void matvec::Individual::pretend_missing ( int on,

const double * gfreq,

const unsigned tng

)

Definition at line 399 of file individual.cpp.
References connect_keeper, initial_anterior(), initial_posterior(), matvec::DataNode::missing, and record().
Referenced by matvec::NuFamily::pretend_missing().

00400 { 00401 if (on) { 00402 if (p_origin) { 00403 record()[0].missing += 1; 00404 initial_anterior(gfreq,tng); 00405 if (connect_keeper == 1) { 00406 initial_posterior(tng,1); 00407 } 00408 else { 00409 initial_posterior(tng); 00410 } 00411 } 00412 else { 00413 initial_posterior(tng,1); 00414 } 00415 } 00416 else { 00417 if (p_origin) record()[0].missing -= 1; 00418 } 00419 }

void matvec::Individual::pretend_multi_m_missing ( int on,

int tng

)

Definition at line 948 of file individual.cpp.
References connect_keeper, initial_multi_m_anterior(), initial_multi_m_posterior(), matvec::DataNode::missing, and record().
Referenced by matvec::NuFamily::pretend_multi_m_missing().

00948 { 00949 if (on) { 00950 if (p_origin) { 00951 record()[0].missing += 1; 00952 initial_multi_m_anterior(tng); 00953 // initial_anterior(gfreq,tng); 00954 if (connect_keeper == 1) { 00955 initial_multi_m_posterior(tng,1); 00956 // initial_posterior(tng,1); 00957 } 00958 else { 00959 initial_multi_m_posterior(tng,-1); 00960 // initial_posterior(tng); 00961 } 00962 } 00963 else { 00964 initial_multi_m_posterior(tng,1); 00965 // initial_posterior(tng,1); 00966 } 00967 } 00968 else { 00969 if (p_origin) record()[0].missing -= 1; 00970 } 00971 }

void matvec::Individual::pretend_multi_missing ( int on,

doubleMatrix & pen

)

Definition at line 849 of file individual.cpp.
References connect_keeper, initial_multi_anterior(), initial_multi_posterior(), matvec::DataNode::missing, and record().
Referenced by matvec::NuFamily::pretend_multi_missing().

00850 { 00851 if (on) { 00852 if (p_origin) { 00853 record()[0].missing += 1; 00854 initial_multi_anterior(pen); 00855 // initial_anterior(gfreq,tng); 00856 if (connect_keeper == 1) { 00857 initial_multi_posterior(1); 00858 // initial_posterior(tng,1); 00859 } 00860 else { 00861 initial_multi_posterior(-1); 00862 // initial_posterior(tng); 00863 } 00864 } 00865 else { 00866 initial_multi_posterior(1); 00867 // initial_posterior(tng,1); 00868 } 00869 } 00870 else { 00871 if (p_origin) record()[0].missing -= 1; 00872 } 00873 }

void matvec::Individual::put_family ( int i ) [inline]

Definition at line 227 of file individual.h.
References family.
Referenced by matvec::Population::build_nufamily().

00227 {family = i;}

void matvec::Individual::put_gametes ( Vector< unsigned > m_g,

Vector< unsigned > p_g

)

Definition at line 1279 of file individual.cpp.
References calc_q(), m_gamete, p_gamete, q_prob, and matvec::Vector< unsigned >::size().
Referenced by matvec::Population::input_descentGraph().

01279 { 01280 // Authors: Matthias Schelling and Rohan L. Fernando 01281 // (1999) 01282 // Contributors: 01283 m_gamete = m_g; 01284 p_gamete = p_g; 01285 if(m_gamete.size()!= p_gamete.size()){ 01286 throw exception("Individual::put_gametes: m_gamete.size()!= p_gamete.size()"); 01287 } 01288 //init q 01289 q_prob = 1.0; 01290 calc_q(); 01291 }

DataNode* matvec::Individual::record ( void ) const [inline]

Definition at line 203 of file individual.h.
Referenced by cal_m_gprobs(), collapse_mix_antpost(), matvec::Population::fetch_families(), get_m_penetrance(), get_mix_penetrance(), get_penetrance(), getAllelePenetrance(), getDisAllelePenetrance(), getDisGenoPenetrance(), getGenoPenetrance(), matvec::NuFamily::multi_m_anterior(), matvec::NuFamily::multi_m_log_likelihood(), matvec::Population::multi_m_log_likelihood_peeling(), matvec::NuFamily::multi_m_posterior(), matvec::NuFamily::multi_sumint_offspring(), pretend_missing(), pretend_multi_m_missing(), pretend_multi_missing(), matvec::Population::record_ind(), and matvec::Population::setup_m_ww().

00203 {return myrecord;}

void matvec::Individual::release ( void )

Definition at line 511 of file individual.cpp.
References genotype_counter, myoffspring, myrecord, numoffs_spouse, posterior, and spouselist.
Referenced by ~Individual().

00512 { 00513 if (myrecord) {delete [] myrecord; myrecord = 0;} 00514 if (spouselist) {delete [] spouselist; spouselist = 0;} 00515 if (posterior) {delete [] posterior; posterior = 0; } 00516 if (myoffspring) {delete [] myoffspring; myoffspring = 0;} 00517 if (numoffs_spouse) { 00518 delete [] numoffs_spouse; numoffs_spouse = 0; 00519 } 00520 if (genotype_counter) { 00521 delete [] genotype_counter; genotype_counter = 0; 00522 } 00523 }

void matvec::Individual::remodel ( Population * P )

Definition at line 258 of file individual.cpp.
References anterior, anterior_iw, est_GV, genome0, genome1, genotype_counter, genotype_id, group_id, inbc, MBV, myfather, mymother, myoffspring, myrecord, mysex, matvec::GeneticDist::nchrom(), matvec::GeneticDist::ntrait(), numchrom, numoffs, numoffs_spouse, numspouse, numtrait, population, posterior, matvec::Population::prior, RBV, matvec::Genome::remodel(), matvec::Vector< double >::resize(), true_GV, and xbzu_val.
Referenced by Individual(), and matvec::Population::resize().

00259 { 00260 population = P; 00261 genotype_id = -1; 00262 numtrait = population->prior->ntrait(); 00263 numchrom = population->prior->nchrom(); 00264 00265 genome0.remodel(population->prior); 00266 genome1.remodel(population->prior); 00267 00268 if (myrecord) { 00269 delete [] myrecord; 00270 myrecord=0; 00271 } 00272 if(numtrait>0){ 00273 myrecord = new DataNode [numtrait]; 00274 } 00275 else { 00276 myrecord = 0; 00277 } 00278 00279 myfather = 0; 00280 mymother = 0; 00281 if (numoffs_spouse) { 00282 delete [] numoffs_spouse; numoffs_spouse = 0; 00283 } 00284 numspouse = 0; 00285 if (myoffspring) { delete [] myoffspring; myoffspring = 0;} 00286 numoffs = 0; 00287 RBV = 0.0; 00288 MBV = 0.0; 00289 inbc = 0.0; 00290 mysex = '.'; 00291 est_GV = 0.0; 00292 true_GV = 0.0; 00293 group_id = 0; 00294 xbzu_val = 0.0; 00295 genotype_counter = 0; 00296 if (posterior) {delete [] posterior; posterior=0;} 00297 anterior_iw = 0; 00298 anterior.resize(0); 00299 }

void matvec::Individual::reset_id ( const unsigned newid ) [inline]

Definition at line 162 of file individual.h.
References myid.
Referenced by matvec::NuFamily::cutting(), and matvec::Population::renum().

00162 {myid = newid;}

void matvec::Individual::sample_haplotypes ( const unsigned )

Definition at line 1327 of file individual.cpp.
References gamete(), m_gamete, p_gamete, population, matvec::ranf(), matvec::Population::RecoVector, and matvec::Population::SLlocus.
Referenced by matvec::Population::calc_log_q_ratio().

01327 { 01328 //sample haplotypes for an SLlocus, 01329 //origin 0 = maternal, 1 = paternal 01330 Vector <unsigned>* gamete = &m_gamete; 01331 if (origin) { 01332 gamete = &p_gamete; 01333 } 01334 //first, go from SLlocus down to locus 1 01335 for (unsigned i = population->SLlocus - 1; i > 0; i--) { 01336 if (ranf() < population->RecoVector(i)) { //do crossover 01337 if ((*gamete)(i+1) == 0) { (*gamete)(i) = 1; } 01338 else { (*gamete)(i) = 0; } 01339 } 01340 else { //no crossover 01341 if ((*gamete)(i+1) == 0) { (*gamete)(i) = 0; } 01342 else { (*gamete)(i) = 1; } 01343 } 01344 } 01345 //then, go from SLlocus up to last locus 01346 for (unsigned i = population->SLlocus; i < (*gamete).size(); i++) { 01347 if (ranf() < population->RecoVector(i)) { //do crossover 01348 if ((*gamete)(i) == 0) { (*gamete)(i+1) = 1; } 01349 else { (*gamete)(i+1) = 0; } 01350 } 01351 else { //no crossover 01352 if ((*gamete)(i) == 0) { (*gamete)(i+1) = 0; } 01353 else { (*gamete)(i+1) = 1; } 01354 } 01355 } 01356 }

void matvec::Individual::sample_self ( int parent_indicator )

Definition at line 1620 of file individual.cpp.
References matvec::Population::calc_prior_descent_graph(), m_gamete, numLoci, p_gamete, population, matvec::ranf(), update_offsprings_founder_alleles(), vec_cutsetval, and vec_prob.
Referenced by matvec::Population::Gibbs_sample().

01620 { 01621 // Authors: Matthias Schelling and Rohan L. Fernando 01622 // (1999) 01623 // Contributors: L. Radu Totir 01624 01625 // parent_indicator = 0 -> maternal 01626 // parent_indicator = 1 -> paternal 01627 Vector <unsigned> *gamete_p; 01628 01629 if(parent_indicator==0){ 01630 gamete_p=&m_gamete; 01631 } 01632 else { 01633 gamete_p=&p_gamete; 01634 } 01635 01636 // Computing the priors 01637 01638 for ( int j=1; j<=numLoci; j++){ 01639 (*gamete_p)(j)=0; 01640 update_offsprings_founder_alleles(); 01641 vec_prob[j-1][0]=population->calc_prior_descent_graph(j); 01642 (*gamete_p)(j)=1; 01643 update_offsprings_founder_alleles(); 01644 vec_prob[j-1][1]=population->calc_prior_descent_graph(j); 01645 } 01646 // Computing the "cutset" values 01647 int j=0; 01648 vec_cutsetval[j][0]=vec_prob[j][0]; 01649 vec_cutsetval[j][1]=vec_prob[j][1]; 01650 for ( int j=1; j<numLoci; j++){ 01651 vec_cutsetval[j][0]= vec_prob[j][0]* 01652 (vec_cutsetval[j-1][0]*(1-population-> RecoVector(j)) 01653 + vec_cutsetval[j-1][1]*(population-> RecoVector(j))); 01654 vec_cutsetval[j][1]= vec_prob[j][1]* 01655 (vec_cutsetval[j-1][1]*(1-population-> RecoVector(j)) 01656 + vec_cutsetval[j-1][0]*(population-> RecoVector(j))); 01657 } 01658 01659 // Sample the last locus from the marginal 01660 01661 j=numLoci-1; 01662 double u = ranf(); 01663 double p1 = vec_cutsetval[j][0]; 01664 double p2 = vec_cutsetval[j][1]; 01665 if (u<(p1/(p1+p2))){ 01666 (*gamete_p)(j+1)=0; 01667 } 01668 else{ 01669 (*gamete_p)(j+1)=1; 01670 } 01671 update_offsprings_founder_alleles(); 01672 01673 // sample the other loci 01674 01675 for ( int j=numLoci-2; j>=0; j--){ 01676 double u = ranf(); 01677 double recomb=0.0; 01678 if((*gamete_p)(j+2)==0){ 01679 recomb=(1-population-> RecoVector(j+1)); 01680 } 01681 else{ 01682 recomb=population-> RecoVector(j+1); 01683 } 01684 double p1= recomb*vec_cutsetval[j][0]; 01685 double p2=(1-recomb)*vec_cutsetval[j][1]; 01686 if (u<(p1/(p1+p2))){ 01687 (*gamete_p)(j+1)=0; 01688 } 01689 else{ 01690 (*gamete_p)(j+1)=1; 01691 } 01692 update_offsprings_founder_alleles(); 01693 } 01694 }

void matvec::Individual::save ( std::ostream & out )

Definition at line 578 of file individual.cpp.
References matvec::Locus::allele, matvec::Genome::chromosome, father_id(), genome0, genome1, matvec::Chromosome::locus, mother_id(), and myid.
Referenced by display().

00579 { 00580 out << " I " << myid << " F " << father_id() << " M " << mother_id(); 00581 out << " Marker Info: "; 00582 out << genome0.chromosome[0].locus[1].allele << " " ; 00583 out << genome1.chromosome[0].locus[1].allele << " " ; 00584 out << genome0.chromosome[0].locus[2].allele << " " ; 00585 out << genome1.chromosome[0].locus[2].allele; 00586 //out << " Switch " << index_sw << " Beta " << bet_sw << " Epl " << eps_sw; 00587 out << std::endl; 00588 }

void matvec::Individual::search_heteroz ( unsigned qtl )

Definition at line 1706 of file individual.cpp.
References matvec::Locus::allele, matvec::Genome::chromosome, genome0, genome1, matvec::Chromosome::locus, mymother, numLoci, and ord_heter.
Referenced by matvec::Model::DGSamplerSetup().

01706 { 01707 // Authors: Fabiano V. Pita and Rohan L. Fernando 01708 // (2003) 01709 // Contributors: L. Radu Totir 01710 01711 int mult = -1; // __1___2___3___qtl___5____6__ 01712 unsigned step = 1; 01713 unsigned endl = 0; 01714 unsigned endr = 0; 01715 unsigned lcs = qtl; 01716 01717 ord_heter = 0; // 0 means individual is not an ordered heterozygous 01718 01719 if (mymother != NULL){ 01720 return; 01721 } 01722 01723 // first goes to the closest left marker 01724 lcs += step * mult; 01725 mult *= -1; 01726 01727 for (;;) { 01728 if (genome0.chromosome[0].locus[lcs-1].allele != genome1.chromosome[0].locus[lcs-1].allele){ 01729 ord_heter = lcs; 01730 break; 01731 } 01732 01733 if (lcs == 1){ //last locus of left side 01734 endl = 1; 01735 } 01736 01737 if (lcs == numLoci){ //last locus of right side 01738 endr = 1; 01739 } 01740 01741 step += 1; 01742 lcs += step*mult; 01743 mult *= -1; 01744 01745 if (lcs > numLoci){ 01746 break; 01747 } 01748 01749 //working just with the right side 01750 if (endl == 1){ 01751 for (int i=lcs; i<= numLoci; i++){ 01752 if (genome0.chromosome[0].locus[lcs-1].allele != genome1.chromosome[0].locus[lcs-1].allele){ 01753 ord_heter = lcs; 01754 break; 01755 } 01756 } 01757 break; 01758 } 01759 01760 //working just with the left side 01761 if (endr == 1){ 01762 for (int i=lcs; i>=1; i--){ 01763 if (genome0.chromosome[0].locus[lcs-1].allele != genome1.chromosome[0].locus[lcs-1].allele){ 01764 ord_heter = lcs; 01765 break; 01766 } 01767 } 01768 break; 01769 } 01770 } 01771 01772 }

void matvec::Individual::set_founder_alleles ( bool )

Definition at line 1358 of file individual.cpp.
References matvec::Population::founder_allele_counter, get_founder(), m_founder, m_gamete, myfather, mymother, numLoci, p_founder, p_gamete, population, matvec::Vector< unsigned >::resize(), and matvec::Vector< unsigned >::size().
Referenced by matvec::Model::DGSamplerSetup(), get_founder(), matvec::Population::M_H_sample_ext(), and update_offsprings_founder_alleles().

01358 { 01359 // Authors: Matthias Schelling and Rohan L. Fernando 01360 // (1999) 01361 // Contributors: L. Radu Totir 01362 01363 // update == 0 -> first pass 01364 // update == 1 -> already done 01365 // Done 01366 // T F 01367 // ________________ 01368 // T | yes yes | 01369 // Update | | 01370 // F | no yes | 01371 // |______________| 01372 // 01373 // This means that we set the founder_alleles from 01374 // the founder_allele_counter only if not already done 01375 // When we are updating, we change only offsprings 01376 01377 // get space if needed 01378 if (m_founder.size() == 0) { 01379 int zero=0; 01380 m_founder.resize(numLoci, zero); 01381 p_founder.resize(numLoci, zero); 01382 } 01383 01384 // if not already done 01385 //if (!m_founder(1)) { 01386 if (!(!update && m_founder(1))) { 01387 if (!m_founder(1) && update) { 01388 std::cout << "should not happen: update = 1, m_founder(1) set" << std::endl; 01389 } 01390 // if founder set m/p_founder to founder_allele_counter 01391 if (mymother == NULL) { 01392 if (!update) { 01393 std::cout << "founder_allele_counter++" << std::endl; 01394 population->founder_allele_counter++; 01395 for (int i=1; i<= numLoci; i++){ 01396 m_founder(i) = population->founder_allele_counter; 01397 p_founder(i) = population->founder_allele_counter+1; 01398 } 01399 population->founder_allele_counter++; 01400 } 01401 } 01402 // if not founder 01403 else { 01404 Vector <unsigned> &mm_founder = mymother->get_founder("mother",update); 01405 Vector <unsigned> &mp_founder = mymother->get_founder("father",update); 01406 Vector <unsigned> &pm_founder = myfather->get_founder("mother",update); 01407 Vector <unsigned> &pp_founder = myfather->get_founder("father",update); 01408 for (int i=1; i <= numLoci; i++){ 01409 if (m_gamete(i) == 0) { 01410 m_founder(i) = mm_founder(i); 01411 } 01412 else { 01413 m_founder(i) = mp_founder(i); 01414 } 01415 if (p_gamete(i) == 0) { 01416 p_founder(i) = pm_founder(i); 01417 } 01418 else { 01419 p_founder(i) = pp_founder(i); 01420 } 01421 } 01422 } 01423 } 01424 }

void matvec::Individual::set_genotype ( const unsigned c,

const unsigned l,

const unsigned a0,

const unsigned a1

)

Definition at line 564 of file individual.cpp.
References matvec::Locus::allele, matvec::Genome::chromosome, genome0, genome1, and matvec::Chromosome::locus.

00566 { 00567 genome0.chromosome[c].locus[l].allele = a0; 00568 genome1.chromosome[c].locus[l].allele = a1; 00569 }

void matvec::Individual::set_switch ( int Nloci )

Definition at line 591 of file individual.cpp.
References matvec::Locus::allele, bet_sw, matvec::Genome::chromosome, eps_sw, genome0, genome1, id(), matvec::Population::ind_name(), index_sw, matvec::Chromosome::locus, myfather, mymother, and population.
Referenced by matvec::Population::set_switches().

00593 { 00594 /* This assigns the switches and gametes to each individual in the population. 00595 By definition, the maternal gamete gets the lower allele number unless it is known 00596 which source the allele came from. 00597 00598 An locus is switchable only in two circumstances: 00599 1) founder animal is heterozgyous at that locus. 00600 2) both parents are heterozygous for the same alleles at that locus 00601 Under all other cases, the source of the allele can be tracked. 00602 Thus, each locus needs to be checked to determine the source of the allele. 00603 00604 */ 00605 int i,j,k,l,allele1,allele2,sire,dam,sireF,sireM,damF,damM,levelS=1,levelEB=1,Ixswitch=0,epl=0,beta=0,temp,tallele; 00606 if (myfather && (mymother == 0)) { 00607 std::cout << "error father known, mother not! for " << population->ind_name(id()) << std::endl; 00608 std::cout << "This program is not designed to handle this yet!\n Please supply a mother with records." << std::endl; 00609 exit(1); 00610 } 00611 if (mymother && (myfather == 0)) { 00612 std::cout << "error mother known, father not! for " << population->ind_name(id()) << std::endl; 00613 std::cout << "This program is not designed to handle this yet! Please supply a father with records." << std::endl; 00614 exit(1); 00615 } 00616 00617 if (myfather == 0) { // animal is a founder 00618 for (j=(Nloci); j > 0; j--) { 00619 if (genome0.chromosome[0].locus[j].allele > genome1.chromosome[0].locus[j].allele) { // swap alleles 00620 temp=genome0.chromosome[0].locus[j].allele; 00621 genome0.chromosome[0].locus[j].allele=genome1.chromosome[0].locus[j].allele; 00622 genome1.chromosome[0].locus[j].allele =temp; 00623 } 00624 if (genome0.chromosome[0].locus[j].allele != genome1.chromosome[0].locus[j].allele) { // switchable 00625 Ixswitch += levelS; 00626 } 00627 levelS *=2; 00628 } 00629 index_sw=Ixswitch; 00630 } 00631 else { // not a founder so find all the alleles from individual and parents 00632 for (j=(Nloci); j>0; j--) { 00633 allele1=genome0.chromosome[0].locus[j].allele; 00634 allele2=genome1.chromosome[0].locus[j].allele; 00635 sireM=myfather->genome0.chromosome[0].locus[j].allele; 00636 sireF=myfather->genome1.chromosome[0].locus[j].allele; 00637 damM=mymother->genome0.chromosome[0].locus[j].allele; 00638 damF=mymother->genome1.chromosome[0].locus[j].allele; 00639 if ((allele1 != allele2) && (((sireF == damF) && (sireM == damM)) || ((sireF == damM) && (sireM == damF)))) { 00640 Ixswitch += levelS; // Locus is switchable !!! 00641 // Check if alleles in correct order if not swap them 00642 if (allele1 > allele2) { 00643 genome1.chromosome[0].locus[j].allele=allele1; 00644 genome0.chromosome[0].locus[j].allele=allele2; 00645 } 00646 } 00647 // Not switchable so determine source of each allele 00648 else if ((allele1 == sireM) && (allele2 == damM)) { 00649 genome0.chromosome[0].locus[j].allele=allele2; 00650 genome1.chromosome[0].locus[j].allele=allele1; 00651 } 00652 else if ((allele1 == sireM) && (allele2 == damF)) { 00653 genome0.chromosome[0].locus[j].allele=allele2; 00654 genome1.chromosome[0].locus[j].allele=allele1; 00655 } 00656 else if ((allele1 == sireF) && (allele2 == damM)) { 00657 genome0.chromosome[0].locus[j].allele=allele2; 00658 genome1.chromosome[0].locus[j].allele=allele1; 00659 } 00660 else if ((allele1 == sireF) && (allele2 == damF)) { 00661 genome0.chromosome[0].locus[j].allele=allele2; 00662 genome1.chromosome[0].locus[j].allele=allele1; 00663 } 00664 else if ((allele2 == sireM) && (allele1 == damM)) { 00665 genome0.chromosome[0].locus[j].allele=allele1; 00666 genome1.chromosome[0].locus[j].allele=allele2; 00667 } 00668 else if ((allele2 == sireM) && (allele1 == damF)) { 00669 genome0.chromosome[0].locus[j].allele=allele1; 00670 genome1.chromosome[0].locus[j].allele=allele2; 00671 } 00672 else if ((allele2 == sireF) && (allele1 == damM)) { 00673 genome0.chromosome[0].locus[j].allele=allele1; 00674 genome1.chromosome[0].locus[j].allele=allele2; 00675 } 00676 else if ((allele2 == sireF) && (allele1 == damF)) { 00677 genome0.chromosome[0].locus[j].allele=allele1; 00678 genome1.chromosome[0].locus[j].allele=allele2; 00679 } 00680 else { 00681 std::cerr << "ERROR ident alleles different from parents - perhaps parent not in pedigree?\n" 00682 << "Id " << allele1 << " " << allele2 << " " << sireM << " " << sireF << " " << damM << " " << damF << std::endl; 00683 throw exception("ERROR ident alleles different from parents - perhaps parent not in pedigree?"); 00684 } 00685 // Now determine epsilon 00686 if (sireM == sireF) 00687 epl += (levelEB*2); 00688 else if ( genome1.chromosome[0].locus[j].allele == sireF) 00689 epl += levelEB; // Paternal allele from father's father 00690 // Now determine beta 00691 if (damM == damF) 00692 beta += (levelEB*2); 00693 else if (genome0.chromosome[0].locus[j].allele == damF) 00694 beta += levelEB; // maternal allele from dam's father 00695 00696 levelS *=2; 00697 levelEB *=3; 00698 } 00699 } 00700 index_sw=Ixswitch; 00701 eps_sw=epl; 00702 bet_sw=beta; 00703 //std::cout << "Switch " << Ixswitch << " Epli " << epl << " beta " << beta << std::endl; 00704 }

void matvec::Individual::setAlleleOriginVectors ( unsigned locus )

void matvec::Individual::setAlleleStateVectors ( unsigned locus )

Referenced by matvec::Population::setAlleleStateVectors().

double matvec::Individual::setFounderHaplotype ( void )

makes sure that in founders the maternal allele is asigned the lower allele state

Definition at line 1897 of file individual.cpp.
References matvec::Locus::allele, matvec::Genome::chromosome, genome0, genome1, matvec::Chromosome::locus, and numLoci.

01898 { 01899 // Authors: L. Radu Totir 01900 // (August, 2004) 01901 // Contributors: 01902 if(mymother){ 01903 throw exception("Individual::setFounderHaplotype(void) called for a non-founder"); 01904 } 01905 else { 01906 for (unsigned j=0;j<numLoci;j++){ 01907 unsigned patAllele = genome0.chromosome[0].locus[j].allele; 01908 unsigned matAllele = genome1.chromosome[0].locus[j].allele; 01909 if (matAllele > patAllele){ 01910 genome0.chromosome[0].locus[j].allele=matAllele; 01911 genome1.chromosome[0].locus[j].allele=patAllele; 01912 } 01913 } 01914 } 01915 }

void matvec::Individual::setPenetrance ( penetranceType p ) [inline]

Definition at line 173 of file individual.h.
References penetrance_f, and matvec::penetranceType.

00173 {penetrance_f = p;}

char matvec::Individual::sex ( void ) const [inline]

Definition at line 190 of file individual.h.
References mysex.
Referenced by matvec::Population::build_nufamily(), matvec::Population::confirm_sex(), matvec::Population::cprob_children(), matvec::Population::display(), and matvec::Population::genotype_dist_peeling().

00190 {return mysex;}

Individual** matvec::Individual::spouses ( void ) const [inline]

Definition at line 209 of file individual.h.
Referenced by matvec::Population::build_nufamily(), matvec::Population::fullsibs_prob(), matvec::Population::get_posterior(), and matvec::Population::partial_iterative_peeling().

00209 {return spouselist;}

void matvec::Individual::t0 ( unsigned SLlocus,

unsigned gender_parent

)

Definition at line 1484 of file individual.cpp.
References m_gamete, p_gamete, and update_offsprings_founder_alleles().
Referenced by apply_SL_transition(), t1(), t2a(), and t2b().

01484 { 01485 //Sobel & Lange T0 rule 01486 if (gender_parent) { 01487 if (p_gamete(SLlocus)){p_gamete(SLlocus)=0;} 01488 else {p_gamete(SLlocus)=1;} 01489 } 01490 else { 01491 if (m_gamete(SLlocus)){m_gamete(SLlocus)=0;} 01492 else {m_gamete(SLlocus)=1;} 01493 } 01494 update_offsprings_founder_alleles(); 01495 return; 01496 }

void matvec::Individual::t1 ( unsigned SLlocus )

Definition at line 1498 of file individual.cpp.
References mymother, myoffspring, numoffs, t0(), and update_offsprings_founder_alleles().
Referenced by apply_SL_transition(), t2a(), and t2b().

01498 { 01499 //Sobel & Lange T1 rule 01500 //get offsprings 01501 for (int i=0; i<numoffs; i++) { 01502 if (myoffspring[i]->mymother == this) { 01503 myoffspring[i]->t0(SLlocus, 0); 01504 } 01505 else { 01506 myoffspring[i]->t0(SLlocus, 1); 01507 } 01508 } 01509 update_offsprings_founder_alleles(); 01510 return; 01511 }

void matvec::Individual::t2a ( unsigned SLlocus )

Definition at line 1513 of file individual.cpp.
References m_gamete, myfather, mymother, myoffspring, numoffs, numspouse, p_gamete, matvec::ranf(), spouselist, t0(), and t1().
Referenced by apply_SL_transition().

01513 { 01514 //Sobel & Lange T2a rule 01515 //choose spouse 01516 Individual *my_spouse = spouselist[unsigned(ranf() * numspouse)]; 01517 //get offsprings 01518 for (int i=0; i<numoffs; i++) { 01519 //check if related with myspouse 01520 if (myoffspring[i]->myfather == my_spouse 01521 || myoffspring[i]->mymother == my_spouse) { 01522 01523 //do t0 for myoffspring for both alleles if they originate in the opposite gender 01524 if (myoffspring[i]->m_gamete(SLlocus) != myoffspring[i]->p_gamete(SLlocus)) { 01525 myoffspring[i]->t0(SLlocus,0); 01526 myoffspring[i]->t0(SLlocus,1); 01527 } 01528 01529 //do t1 for myoffspring 01530 myoffspring[i]->t1(SLlocus); 01531 } 01532 } 01533 return; 01534 }

void matvec::Individual::t2b ( unsigned SLlocus )

Definition at line 1536 of file individual.cpp.
References m_gamete, myfather, mymother, myoffspring, numoffs, numspouse, p_gamete, matvec::ranf(), spouselist, t0(), and t1().
Referenced by apply_SL_transition().

01536 { 01537 //Sobel & Lange T2b rule 01538 //choose spouse 01539 Individual *my_spouse = spouselist[unsigned(ranf() * numspouse)]; 01540 //get offsprings 01541 for (int i=0; i<numoffs; i++) { 01542 //check if related with myspouse 01543 if (myoffspring[i]->myfather == my_spouse 01544 || myoffspring[i]->mymother == my_spouse) { 01545 01546 //do t0 for myoffspring for both alleles if they originate in the same gender 01547 if (myoffspring[i]->m_gamete(SLlocus) == myoffspring[i]->p_gamete(SLlocus)) { 01548 myoffspring[i]->t0(SLlocus,0); 01549 myoffspring[i]->t0(SLlocus,1); 01550 } 01551 01552 //do t1 for myoffspring 01553 myoffspring[i]->t1(SLlocus); 01554 } 01555 } 01556 return; 01557 }

int matvec::Individual::terminal ( ) const [inline]

Definition at line 158 of file individual.h.
References numoffs.

00158 {return !numoffs;}

void matvec::Individual::update_offsprings_founder_alleles ( void )

Definition at line 1437 of file individual.cpp.
References myoffspring, numoffs, and set_founder_alleles().
Referenced by matvec::Population::calc_log_q_ratio(), sample_self(), t0(), and t1().

01437 { 01438 set_founder_alleles(1); //1 invokes updating 01439 //do all ofsprings 01440 if (numoffs) { 01441 for (int i=0; i<numoffs; i++) { 01442 myoffspring[i]->update_offsprings_founder_alleles(); 01443 } 01444 } 01445 }

double matvec::Individual::xbzu ( void ) const [inline]

Definition at line 176 of file individual.h.
References xbzu_val.

00176 {return xbzu_val;}

void matvec::Individual::xbzu ( const double x ) [inline]

Definition at line 168 of file individual.h.
References xbzu_val.
Referenced by matvec::Model::setup_ww(), and matvec::Model::setup_ww_single_trait().

00168 {xbzu_val = x;}

Friends And Related Function Documentation

friend class NuFamily [friend]

Definition at line 114 of file individual.h.

ostream& operator<< ( ostream & stream,

Individual & i

) [friend]

friend class Population [friend]

Definition at line 113 of file individual.h.

Member Data Documentation

Vector<double> matvec::Individual::anterior

Definition at line 147 of file individual.h.
Referenced by matvec::Population::anterior(), matvec::NuFamily::anterior(), collapse_antpost(), collapse_mix_antpost(), copyfrom(), matvec::Population::genotype_dist_peeling(), initial_anterior(), matvec::NuFamily::log_likelihood(), matvec::Population::maxant_maxpost(), matvec::Population::maxant_maxpost_old(), matvec::Population::posterior(), matvec::NuFamily::posterior(), and remodel().

double matvec::Individual::anterior_iw

Definition at line 148 of file individual.h.
Referenced by matvec::NuFamily::cutting(), initial_anterior(), matvec::NuFamily::multi_ant_post(), matvec::NuFamily::multi_initialize(), matvec::NuFamily::multi_m_ant_post(), matvec::NuFamily::multi_m_initialize(), matvec::Population::partial_iterative_peeling(), and remodel().

int matvec::Individual::assigned_founder_allele

Definition at line 270 of file individual.h.
Referenced by matvec::Population::build_connected_groups(), copyfrom(), Individual(), and matvec::Population::process_alleles_neighbors().

int matvec::Individual::bet_sw [protected]

Definition at line 127 of file individual.h.
Referenced by copyfrom(), matvec::NuFamily::multi_anterior(), matvec::NuFamily::multi_fullsibs_prob(), matvec::NuFamily::multi_get_tr(), matvec::NuFamily::multi_m_anterior(), and set_switch().

BG matvec::Individual::bgDMPDQ

Definition at line 289 of file individual.h.
Referenced by map_pdq().

BG matvec::Individual::bgSMPDQ

Definition at line 289 of file individual.h.
Referenced by map_pdq().

int matvec::Individual::connect_keeper [protected]

Definition at line 124 of file individual.h.
Referenced by matvec::Population::break_loop(), copyfrom(), matvec::NuFamily::cutting(), Individual(), pretend_missing(), pretend_multi_m_missing(), and pretend_multi_missing().

unsigned matvec::Individual::currentLocus [static]

Definition at line 35 of file individual.cpp.
Referenced by getAlleleMTransmissionProb(), getAllelePenetrance(), getAllelePTransmissionProb(), getDisAllelePenetrance(), getDisGenoPenetrance(), getMTransmissionProb(), getPTransmissionProb(), matvec::Population::initAlleleNodeList(), and matvec::Population::initGenotypeNodeList().

int matvec::Individual::eps_sw [protected]

Definition at line 127 of file individual.h.
Referenced by copyfrom(), matvec::NuFamily::multi_anterior(), matvec::NuFamily::multi_fullsibs_prob(), matvec::NuFamily::multi_get_tr(), matvec::NuFamily::multi_m_anterior(), and set_switch().

double matvec::Individual::est_GV

Definition at line 144 of file individual.h.
Referenced by matvec::Population::break_loop(), copyfrom(), matvec::Population::genotype_dist_peeling(), matvec::Model::genotypic_value_peeling(), matvec::Model::graph_log_likelihood_peeling(), Individual(), matvec::Model::log_likelihood_peeling(), matvec::Population::maxant_maxpost(), matvec::Population::maxant_maxpost_old(), matvec::Population::multi_geno_dist_peeling(), matvec::Population::multi_m_geno_dist_peeling(), and remodel().

int matvec::Individual::family [protected]

Definition at line 128 of file individual.h.
Referenced by copyfrom(), get_family(), and put_family().

doubleMatrix matvec::Individual::g_weight [static]

Definition at line 30 of file individual.cpp.
Referenced by cal_m_gprobs(), collapse_mix_antpost(), and matvec::Population::maxant_maxpost().

Vector<double>* matvec::Individual::genotype_counter [protected]

Definition at line 133 of file individual.h.
Referenced by copyfrom(), matvec::Population::count_genotype(), matvec::Population::display(), Individual(), release(), matvec::Population::release_genotype_counter(), remodel(), and matvec::Population::resize_genotype_counter().

doubleMatrix matvec::Individual::genotype_freq1

Definition at line 267 of file individual.h.
Referenced by matvec::Population::sum_genotype_freq1().

doubleMatrix matvec::Individual::genotype_freq2

Definition at line 268 of file individual.h.
Referenced by matvec::Population::sum_genotype_freq2().

int matvec::Individual::genotype_id

Definition at line 143 of file individual.h.
Referenced by copyfrom(), genotypic_val(), get_penetrance(), Individual(), and remodel().

Vector<double> matvec::Individual::gprobs [protected]

Definition at line 129 of file individual.h.
Referenced by cal_gprobs(), cal_m_gprobs(), collapse_mix_antpost(), and copyfrom().

Vector<unsigned> matvec::Individual::id_pdq

Definition at line 276 of file individual.h.
Referenced by get_id_pdq(), and matvec::Population::M_H_sample_ext().

Vector<unsigned> matvec::Individual::id_pdq1

Definition at line 276 of file individual.h.
Referenced by matvec::Population::M_H_sample_ext().

double matvec::Individual::inbc [protected]

Definition at line 131 of file individual.h.
Referenced by copyfrom(), inbcoef(), matvec::Population::inbcoef_meuwissen(), matvec::Population::inbcoef_quaas(), Individual(), and remodel().

int matvec::Individual::index_sw [protected]

Definition at line 127 of file individual.h.
Referenced by copyfrom(), initial_multi_anterior(), initial_multi_posterior(), matvec::NuFamily::multi_anterior(), matvec::NuFamily::multi_fullsibs_prob(), matvec::NuFamily::multi_get_tr(), matvec::NuFamily::multi_m_anterior(), matvec::NuFamily::multi_m_posterior(), matvec::NuFamily::multi_sumint_offspring(), n_switches(), and set_switch().

unsigned matvec::Individual::initial_order1

Definition at line 279 of file individual.h.
Referenced by get_allele_v1().

unsigned matvec::Individual::initial_order2

Definition at line 279 of file individual.h.
Referenced by get_allele_v1().

double matvec::Individual::isqrt2pi = 1.0/std::sqrt(6.283185308) [static]

Definition at line 37 of file individual.cpp.
Referenced by getAllelePenetrance(), and getGenoPenetrance().

int matvec::Individual::loop_connector

Definition at line 141 of file individual.h.
Referenced by copyfrom(), matvec::NuFamily::cutting(), Individual(), matvec::NuFamily::multi_ant_post(), matvec::NuFamily::multi_m_ant_post(), and matvec::Population::peeling_sequence().

Dblock matvec::Individual::m_anterior

Definition at line 220 of file individual.h.
Referenced by cal_gprobs(), collapse_antpost(), copyfrom(), initial_multi_anterior(), matvec::NuFamily::multi_anterior(), matvec::NuFamily::multi_llh(), and matvec::NuFamily::multi_posterior().

int matvec::Individual::m_anterior_iw

Definition at line 219 of file individual.h.
Referenced by initial_multi_anterior().

double matvec::Individual::m_anterior_scale

Definition at line 222 of file individual.h.
Referenced by copyfrom(), initial_multi_anterior(), matvec::NuFamily::multi_anterior(), matvec::NuFamily::multi_llh(), matvec::NuFamily::multi_posterior(), and matvec::Population::multipoint_likelihood().

unsigned matvec::Individual::m_counter

Definition at line 249 of file individual.h.
Referenced by matvec::Population::output_pdq(), and matvec::Population::sum_descentState().

Vector<unsigned> matvec::Individual::m_counter_map

Definition at line 290 of file individual.h.
Referenced by matvec::Model::DGSamplerSetup(), and matvec::Population::sum_descentState_map().

Vector<unsigned> matvec::Individual::m_founder

Definition at line 245 of file individual.h.
Referenced by matvec::Population::build_connected_groups(), matvec::Population::build_founder_allele_neighbors(), get_allele_v1(), get_founder(), matvec::Population::process_alleles_neighbors(), set_founder_alleles(), matvec::Population::update_allele_vectors(), and matvec::Population::update_ibdMatrix().

Vector<unsigned> matvec::Individual::m_gamete1

Definition at line 244 of file individual.h.
Referenced by matvec::Population::calc_log_q_ratio(), matvec::Population::M_H_sample_ext(), and matvec::Population::show_change().

Vector<unsigned> matvec::Individual::m_gameteOld

Definition at line 299 of file individual.h.
Referenced by matvec::Population::setupRSampler(), and matvec::Population::storeSampledGametes().

Matrix<unsigned> matvec::Individual::m_haplotype

Definition at line 285 of file individual.h.
Referenced by count_haplotype(), display_freq_haplotype(), and map_pdq().

Public Methods
	Individual (void)
	Individual (Population *P)
	Individual (const Individual &A)
	~Individual (void)
const Individual &	operator= (const Individual &A)
int	terminal () const
int	base () const
int	isolated () const
void	reset_id (const unsigned newid)
void	release (void)
void	remodel (Population *P)
void	gamete (Chromosome *C, const int n, const double r) const
void	display ()
void	save (std::ostream &out)
void	xbzu (const double x)
void	initial_anterior (const double *gfreq, const unsigned tng, const int cond=-1)
void	initial_posterior (const unsigned tng, const int cond=-1)
void	pretend_missing (int on, const double *gfreq, const unsigned tng)
void	setPenetrance (penetranceType p)
double	get_penetrance (Vector< double > &pen)
double	xbzu (void) const
double	genotypic_val (void) const
double	inbcoef (void) const
double	father_inbcoef (void) const
double	mother_inbcoef (void) const
unsigned	nchrom (void) const
unsigned	family_id (void)
unsigned	marked (void) const
unsigned	id (void) const
unsigned	nspouse (void) const
unsigned	noffs (void) const
const unsigned *	noffs_spouse (void) const
char	sex (void) const
unsigned	gid (void) const
unsigned	paternal_chrom_id (const unsigned c) const
unsigned	maternal_chrom_id (const unsigned c) const
unsigned	father_id (void) const
unsigned	mother_id (void) const
unsigned	father_gid (void) const
unsigned	mother_gid (void) const
DataNode *	record (void) const
Chromosome *	paternal_chrom (void)
Chromosome *	maternal_chrom (void)
Individual *	father (void) const
Individual *	mother (void) const
Individual **	offspring (void) const
Individual **	spouses (void) const
void	genotype (const unsigned c, const unsigned l, unsigned gtype[]) const
void	set_genotype (const unsigned c, const unsigned l, const unsigned a0, const unsigned a1)
void	set_switch (int Nloci)
void	initial_multi_anterior (doubleMatrix &penetrance)
void	initial_multi_posterior (const int cond)
void	collapse_antpost (void)
unsigned	n_switches (void)
double	get_m_penetrance (doubleMatrix &pen)
void	pretend_multi_missing (int on, doubleMatrix &pen)
void	put_family (int i)
int	get_family (void)
void	cal_gprobs (Dblock &post_mat_f)
Vector< double >	get_gprobs (void)
double	get_m_posterior (int excJ,Dblock &post_mat)
void	initial_multi_m_posterior (const unsigned tn_qtl, const int cond)
void	initial_multi_m_anterior (const unsigned tn_qtl)
void	pretend_multi_m_missing (int on, int tng)
void	cal_m_gprobs (int tng)
void	collapse_mix_antpost (void)
double	get_mix_penetrance (Vector< double > &pen)
void	put_gametes (Vector< unsigned > m_g, Vector< unsigned > p_g)
void	set_founder_alleles (bool)
Vector< unsigned > &	get_founder (std::string, bool)
void	update_offsprings_founder_alleles (void)
void	t0 (unsigned SLlocus, unsigned gender_parent)
void	t1 (unsigned SLlocus)
void	t2a (unsigned SLlocus)
void	t2b (unsigned SLlocus)
void	apply_SL_transition (const unsigned rule, const unsigned lcs)
void	apply_SL_cascade (const unsigned rule, const unsigned SLlocus)
double	graph_trans_prob (unsigned, unsigned, unsigned)
double	calc_q (void)
	method to calc q prob for individual; q is stored in 1 variable
void	sample_haplotypes (const unsigned)
void	sample_self (int parent_indicator)
Vector< unsigned >	get_id_pdq (void)
void	search_heteroz (unsigned qtl)
void	get_allele_v1 (unsigned lcs, Vector< int > allele_vector1)
void	count_haplotype (void)
void	display_freq_haplotype (unsigned)
void	map_pdq (int samples, int interval, double r_aq, double r_bq)
void	map_pdq (int samples, int interval, BG r_aq, BG r_bq)
void	parents (void)
unsigned	allAllelesForLocus (unsigned j)
unsigned	allGenosForLocus (unsigned j)
double	getAllelePenetrance (void)
	returns the allele penetrance for the RSampler
double	getDisAllelePenetrance (void)
double	getAllelePenetrance (unsigned forLocus)
double	getDisAllelePenetrance (unsigned forLocus)
double	getGenoPenetrance (void)
	returns the genotype penetrance for the RSampler
double	getDisGenoPenetrance (void)
double	getAlleleMTransmissionProb (void)
	returns the transmission probability of a maternal allele when the allele origin is assumed known. Used when we peel across pedigree and loci jointly.
double	getAllelePTransmissionProb (void)
	returns the transmission probability of a paternal allele when the allele origin is assumed known. Used when we peel across pedigree and loci jointly.
double	getAlleleMRTransmissionProb (unsigned forLocus)
double	getAllelePRTransmissionProb (unsigned forLocus)
double	getTransitionProb (void)
	returns the genotype transition probability in the RSampler
double	getMTransmissionProb (void)
	returns the maternal allele transmission probability for the RSampler for genotype peeling
double	getPTransmissionProb (void)
	returns the paternal allele transmission probability for the RSampler for genotype peeling
double	getTransmissionProb (unsigned iA, unsigned mA, unsigned pA, Vector< unsigned > &gamete)
double	getMatthiasTransitionProb (void)
double	getMatthiasMTransmissionProb (void)
double	getMatthiasPTransmissionProb (void)
double	getMatthiasTransmissionProb (unsigned iA, unsigned mA, unsigned pA, Vector< unsigned > &gamete, Vector< unsigned > &gameteOld)
int	findLeftLocus (Vector< unsigned > &gamete)
int	findRightLocus (Vector< unsigned > &gamete)
void	setFounderHaplotype (void)
	makes sure that in founders the maternal allele is asigned the lower allele state
void	displayGenotypes (unsigned locus)
void	displayAlleleVectors (unsigned locus)
void	setAlleleStateVectors (unsigned locus)
void	setAlleleOriginVectors (unsigned locus)
Public Attributes
int	loop_connector
int	p_origin
unsigned	group_id
int	genotype_id
double	RBV
double	MBV
double	est_GV
double	true_GV
double	xbzu_val
DataNode *	myrecord
Vector< double >	anterior
Vector< double > *	posterior
Vector< double >	posterior_iw
double	anterior_iw
doubleMatrix *	residual_var
int	m_anterior_iw
Dblock	m_anterior
Vector< Dblock >	m_posterior
double	m_anterior_scale
Vector< double >	m_posterior_scale
Vector< Vector< UNormal > >	mix_anterior
Vector< Mixed_post_vec >	mix_posterior
Vector< unsigned >	m_gamete
Vector< unsigned >	m_gamete1
Vector< unsigned >	p_gamete
Vector< unsigned >	p_gamete1
Vector< unsigned >	m_founder
Vector< unsigned >	p_founder
unsigned	p_counter
unsigned	m_counter
int	marker_index
double	q_prob
doubleMatrix	genotype_freq1
doubleMatrix	genotype_freq2
int ***	mode_matrix
int	assigned_founder_allele
Vector< unsigned >	id_pdq
Vector< unsigned >	id_pdq1
unsigned	ord_heter
unsigned	initial_order1
unsigned	initial_order2
Matrix< unsigned >	m_haplotype
Matrix< unsigned >	p_haplotype
double	mm_pdq
double	mp_pdq
double	pm_pdq
double	pp_pdq
BG	bgDMPDQ
BG	bgSMPDQ
Vector< unsigned >	m_counter_map
Vector< unsigned >	p_counter_map
SafeSTLVector< unsigned >	matHaplotypeCount
SafeSTLVector< unsigned >	patHaplotypeCount
Vector< unsigned >	m_gameteOld
Vector< unsigned >	p_gameteOld
SafeSTLVector< GenotypeNode >	genotNodeVector
SafeSTLVector< AlleleStateNode >	malleleStateNodeVector
SafeSTLVector< AlleleStateNode >	palleleStateNodeVector
SafeSTLVector< AlleleOriginNode >	malleleOriginNodeVector
SafeSTLVector< AlleleOriginNode >	palleleOriginNodeVector
Vector< Vector< double > >	mHaplotypeFreq
Vector< Vector< double > >	pHaplotypeFreq
Static Public Attributes
Population *	population
doubleMatrix	g_weight
std::vector< std::vector< double > >	vec_prob
std::vector< std::vector< double > >	vec_cutsetval
SafeSTLVector< unsigned >	QTLPosVector
unsigned	numLoci
unsigned	currentLocus
unsigned	nQTL
double	isqrt2pi = 1.0/std::sqrt(6.283185308)
Protected Methods
void	copyfrom (const Individual &A)
Protected Attributes
unsigned	myid
unsigned	numchrom
unsigned	numoffs
unsigned	numspouse
unsigned	numtrait
unsigned *	numoffs_spouse
Individual *	myfather
Individual *	mymother
Individual **	myoffspring
Individual **	spouselist
penetranceType	penetrance_f
char	mysex
int	connect_keeper
int	index_sw
int	bet_sw
int	eps_sw
int	family
Vector< double >	gprobs
double	inbc
Genome	genome0
Genome	genome1
Vector< double > *	genotype_counter
std::set< Individual * >	offs_tree
std::list< NuFamily * >	related_family
Friends
class	Population
class	NuFamily
ostream &	operator<< (ostream &stream, Individual &i)