void DosageCalculator::CalculateMarkerInfo(int marker, double& freq, double& maf, double& avgPost, double& rsq)
{
if (stored == 0) return;
if (!storeDistribution) return;
double scale_sg = 1.0 / (samples * genotypes + 1e-30);
double scale_g = 1.0 / (genotypes + 1e-30);
double scale_ss = 1.0 / (samples * samples + 1e-30);
double p0 = 0.0, p1 = 0.0;
double qc = 0.0, sumsq = 0.0;
for (int sample = 0; sample < genotypes; sample++)
{
unsigned int n0, n1, n2;
GetCounts(sample, marker, n0, n1, n2);
p0 += n0; p1 += n1;
qc += (n0 > n1 && n0 > n2) ? n0 : (n1 > n2) ? n1 : n2;
sumsq += square(n0 + n1 * 0.5) * scale_ss;
}
p0 *= scale_sg; p1 *= scale_sg;
qc *= scale_sg; sumsq *= scale_g;
freq = p0 + p1 * 0.50;
maf = freq > 0.50 ? 1.0-freq : freq;
double var1 = max(p0 + p1 * 0.25 - square(freq), 0);
double var2 = max(sumsq - square(freq), 0);
avgPost = qc;
rsq = var2 / (var1 + 1e-30);
}
void DosageCalculator::OutputMarkerInfo(FILE * output)
{
if (stored == 0) return;
if (!storeDistribution)
{
OutputBasicMarkerInfo(output);
return;
}
fprintf(output, "SNP\tAl1\tAl2\tFreq1\tMAF\tQuality\tRsq\n");
double scale_sg = 1.0 / (samples * genotypes + 1e-30);
double scale_g = 1.0 / (genotypes + 1e-30);
double scale_ss = 1.0 / (samples * samples + 1e-30);
for (int marker = 0; marker < markers; marker++)
{
double p0 = 0.0, p1 = 0.0;
double qc = 0.0, sumsq = 0.0;
for (int sample = 0; sample < genotypes; sample++)
{
unsigned int n0, n1, n2;
GetCounts(sample, marker, n0, n1, n2);
p0 += n0; p1 += n1;
qc += (n0 > n1 && n0 > n2) ? n0 : (n1 > n2) ? n1 : n2;
sumsq += square(n0 + n1 * 0.5) * scale_ss;
}
p0 *= scale_sg; p1 *= scale_sg;
qc *= scale_sg; sumsq *= scale_g;
double freq = p0 + p1 * 0.50;
double var1 = max(p0 + p1 * 0.25 - square(freq), 0);
double var2 = max(sumsq - square(freq), 0);
MarkerInfo * info = Pedigree::GetMarkerInfo(marker);
fprintf(output, "%s\t%s\t%s\t%.4f\t%.4f\t%.4f\t%.4f\n",
(const char *) info->name,
(const char *) info->GetAlleleLabel(1),
info->CountAlleles() > 1 ? (const char *) info->GetAlleleLabel(2) : "-",
freq, freq > 0.50 ? 1.0 - freq : freq, qc, var2 / (var1 + 1e-30));
}
}
double DosageCalculator::GetQuality(int individual, int genotype)
{
if (stored == 0) return 0.0;
unsigned int n2, n1, n0;
GetCounts(individual, genotype, n0, n1, n2);
if (n0 >= n2 && n0 >= n1)
return n0 / (double) stored;
if (n1 >= n2)
return n1 / (double) stored;
return n2 / (double) stored;
}
int DosageCalculator::GetBestGenotype(int individual, int genotype)
{
if (stored == 0) return 1;
unsigned int n2, n1, n0;
GetCounts(individual, genotype, n0, n1, n2);
if (n0 >= n2 && n0 >= n1)
return 0;
if (n1 >= n2)
return 1;
return 2;
}
int main(int argc, char *argv[]){
SetStyle();
bool use_mc(false);
char opt(' ');
while(( opt=getopt(argc, argv, "m") )!=-1){
switch(opt){
case 'm':
use_mc=true;
break;
default:
break;
}
}
{TTree crap;}
std::vector<std::string> observed_names(0), signal_names;
signal_names.push_back("raw_plots_and_values/SMS-TChiHH_2b2b_2J_mChargino-400_mLSP-1_TuneZ2star_8TeV-madgraph-tauola_Summer12-START53_V19_FSIM-v1_AODSIM_UCSB1871_v71_SyncSkim.root");
if(use_mc){
observed_names.push_back("raw_plots_and_values/BJets_HT-1000ToInf_8TeV-madgraph_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1895_v71_SyncSkim.root");//6
observed_names.push_back("raw_plots_and_values/BJets_HT-250To500_8TeV-madgraph_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1893_v71_SyncSkim.root");//7
observed_names.push_back("raw_plots_and_values/BJets_HT-500To1000_8TeV-madgraph_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1894_v71_SyncSkim.root");//8
observed_names.push_back("raw_plots_and_values/TTJets_FullLeptMGDecays_8TeV-madgraph-tauola_Summer12_DR53X-PU_S10_START53_V7C-v2_AODSIM_UCSB1883_v71_SyncSkim.root");//9
observed_names.push_back("raw_plots_and_values/TTJets_SemiLeptMGDecays_8TeV-madgraph-tauola_Summer12_DR53X-PU_S10_START53_V7C-v1_AODSIM_UCSB1884_v71_SyncSkim.root");//10
observed_names.push_back("raw_plots_and_values/TTJets_HadronicMGDecays_8TeV-madgraph_Summer12_DR53X-PU_S10_START53_V7A_ext-v1_AODSIM_UCSB1880_v71_SyncSkim.root");//11
observed_names.push_back("raw_plots_and_values/TTH_HToBB_M-125_8TeV-pythia6_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1855_v71_SyncSkim.root");//12
observed_names.push_back("raw_plots_and_values/TTWJets_8TeV-madgraph_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1857_v71_SyncSkim.root");//13
observed_names.push_back("raw_plots_and_values/TTZJets_8TeV-madgraph_v2_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1856_v71_SyncSkim.root");//14
observed_names.push_back("raw_plots_and_values/Tbar_s-channel_TuneZ2star_8TeV-powheg-tauola_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1864_v71_SyncSkim.root");//15
observed_names.push_back("raw_plots_and_values/Tbar_t-channel_TuneZ2star_8TeV-powheg-tauola_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1865_v71_SyncSkim.root");//16
observed_names.push_back("raw_plots_and_values/Tbar_tW-channel-DR_TuneZ2star_8TeV-powheg-tauola_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1866_v71_SyncSkim.root");//17
observed_names.push_back("raw_plots_and_values/T_s-channel_TuneZ2star_8TeV-powheg-tauola_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1860_v71_SyncSkim.root");//18
observed_names.push_back("raw_plots_and_values/T_t-channel_TuneZ2star_8TeV-powheg-tauola_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1861_v71_SyncSkim.root");//19
observed_names.push_back("raw_plots_and_values/T_tW-channel-DR_TuneZ2star_8TeV-powheg-tauola_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1862_v71_SyncSkim.root");//20
observed_names.push_back("raw_plots_and_values/W2JetsToLNu_TuneZ2Star_8TeV-madgraph_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1877_v71_SyncSkim.root");//21
observed_names.push_back("raw_plots_and_values/W3JetsToLNu_TuneZ2Star_8TeV-madgraph_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1878_v71_SyncSkim.root");//22
observed_names.push_back("raw_plots_and_values/W4JetsToLNu_TuneZ2Star_8TeV-madgraph_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1879_v71_SyncSkim.root");//23
observed_names.push_back("raw_plots_and_values/ZJetsToNuNu_100_HT_200_TuneZ2Star_8TeV_madgraph_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1887_v71_SyncSkim.root");//24
observed_names.push_back("raw_plots_and_values/ZJetsToNuNu_200_HT_400_TuneZ2Star_8TeV_madgraph_ext_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1889_v71_SyncSkim.root");//25
observed_names.push_back("raw_plots_and_values/ZJetsToNuNu_200_HT_400_TuneZ2Star_8TeV_madgraph_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1888_v71_SyncSkim.root");//26
observed_names.push_back("raw_plots_and_values/ZJetsToNuNu_400_HT_inf_TuneZ2Star_8TeV_madgraph_ext_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1891_v71_SyncSkim.root");//27
observed_names.push_back("raw_plots_and_values/ZJetsToNuNu_400_HT_inf_TuneZ2Star_8TeV_madgraph_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1890_v71_SyncSkim.root");//28
observed_names.push_back("raw_plots_and_values/WH_WToLNu_HToBB_M-125_8TeV-powheg-herwigpp_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1858_v71_SyncSkim.root");//29
observed_names.push_back("raw_plots_and_values/ZH_ZToBB_HToBB_M-125_8TeV-powheg-herwigpp_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1868_v71_SyncSkim.root");//30
observed_names.push_back("raw_plots_and_values/WW_TuneZ2star_8TeV_pythia6_tauola_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1874_v71_SyncSkim.root");//31
observed_names.push_back("raw_plots_and_values/ZZ_TuneZ2star_8TeV_pythia6_tauola_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1876_v71_SyncSkim.root");//32
observed_names.push_back("raw_plots_and_values/WbbJetsToLNu_Massive_TuneZ2star_8TeV-madgraph-pythia6_tauola_Summer12_DR53X-PU_S10_START53_V7A-v1_AODSIM_UCSB1859_v71_SyncSkim.root");//33
}else{
observed_names.push_back("raw_plots_and_values/MET_Run2012A-13Jul2012-v1_AOD_UCSB1852_v71_SyncSkim.root");//0
observed_names.push_back("raw_plots_and_values/MET_Run2012B-13Jul2012-v1_AOD_UCSB1853_v71_SyncSkim.root");//1
observed_names.push_back("raw_plots_and_values/MET_Run2012C-24Aug2012-v1_AOD_UCSB1854_v71_SyncSkim.root");//2
observed_names.push_back("raw_plots_and_values/MET_Run2012C-PromptReco-v2_AOD_UCSB1867_v71_SyncSkim.root");//3
observed_names.push_back("raw_plots_and_values/MET_Run2012D-PromptReco-v1_AOD_UCSB1869_v71_SyncSkim.root");//4
observed_names.push_back("raw_plots_and_values/MET_Run2012D-PromptReco-v1_AOD_UCSB1870_v71_SyncSkim.root");//5
}
std::vector<TFile*> observed_files(0), signal_files(0);
GetFiles(observed_files, observed_names);
GetFiles(signal_files, signal_names);
std::vector<TTree*> observed_trees(0), signal_trees(0);
GetTrees(observed_trees, observed_files);
GetTrees(signal_trees, signal_files);
WeightCalculator weightCalc(19399.0);
std::vector<double> observed_weights(0), signal_weights;
GetWeights(observed_weights, observed_names, weightCalc);
GetWeights(signal_weights, signal_names, weightCalc);
std::vector<ABCDCount> observed_counts(0), signal_counts;
GetCounts(observed_counts, observed_trees, observed_weights);
GetCounts(signal_counts, signal_trees, signal_weights);
KillTrees(observed_trees);
KillTrees(signal_trees);
KillFiles(observed_files);
KillFiles(signal_files);
ABCDCalculator abcd_calculator(observed_counts, signal_counts);
const unsigned int num_params(abcd_calculator.GetNumberOfParameters());
TMinuit minuit(num_params);
minuit.SetPrintLevel(1);
double strategy[1]={2.0};
int useless(0);
minuit.mnexcm("SET STR", strategy, 1, useless);
MinuitFunctor<ABCDCalculator>::SetFunctor(&abcd_calculator);
MinuitFunctor<ABCDCalculator>::SetNumParams(num_params);
minuit.SetFCN(MinuitFunctor<ABCDCalculator>::Function);
minuit.SetMaxIterations(std::numeric_limits<int32_t>::max());
std::cout << "before" << std::endl;
for(unsigned int i(0); i<num_params; ++i){
SetParameter(i, num_params, minuit);
}
std::cout << "middle" << std::endl;
minuit.Migrad();
minuit.Migrad();
minuit.Migrad();
minuit.mnmnos();
minuit.mnmnos();
minuit.mnmnos();
std::cout << "after" << std::endl;
}
