void FidoInterface::getEstimated_and_Empirical_FDR(
const std::vector<std::vector<string> >& proteinNames,
const std::vector<double>& probabilities,
std::vector<double>& empq,
std::vector<double>& estq) {
empq.clear();
estq.clear();
std::vector<std::pair<double, bool> > combined;
std::vector<double> peps;
for (unsigned int k = 0; k < proteinNames.size(); ++k) {
double prob = probabilities[k];
unsigned tpChange = countTargets(proteinNames[k]);
unsigned fpChange = proteinNames[k].size() - tpChange;
bool isDecoy = (tpChange == 0);
combined.push_back(make_pair(probabilities[k], !isDecoy));
peps.push_back(probabilities[k]);
}
if (usePi0_) {
std::vector<double> pvals;
PosteriorEstimator::getPValues(combined, pvals);
pi0_ = PosteriorEstimator::estimatePi0(pvals);
}
PosteriorEstimator::setNegative(true); // also get q-values for decoys
PosteriorEstimator::getQValuesFromPEP(peps, estq);
PosteriorEstimator::getQValues(pi0_, combined, empq);
}
void FidoInterface::getEstimated_and_Empirical_FDR(
const std::vector<std::vector<string> >& proteinNames,
const std::vector<double>& probabilities,
std::vector<double>& empq,
std::vector<double>& estq) {
empq.clear();
estq.clear();
double targetDecoyRatio = 1.0;
if (usePi0_) {
targetDecoyRatio = static_cast<double>(numberTargetProteins_) / numberDecoyProteins_;
std::vector<std::pair<double, bool> > combined;
for (unsigned int k = 0; k < proteinNames.size(); ++k) {
double prob = probabilities[k];
unsigned tpChange = countTargets(proteinNames[k]);
unsigned fpChange = proteinNames[k].size() - tpChange;
bool isDecoy = (tpChange == 0);
combined.push_back(make_pair(probabilities[k], !isDecoy));
}
std::vector<double> pvals;
PosteriorEstimator::getPValues(combined, pvals);
pi0_ = PosteriorEstimator::estimatePi0(pvals);
}
FDRCalculator fdrCalculator(usePi0_, targetDecoyRatio, pi0_ * absenceRatio_, countDecoyQvalue_);
//NOTE no need to store more q values since they will not be taken into account while estimating MSE FDR divergence
for (unsigned int k = 0; (k < proteinNames.size() &&
(fdrCalculator.getPreviousEstQ() <= mseThreshold_)); k++) {
double prob = probabilities[k];
unsigned tpChange = countTargets(proteinNames[k]);
unsigned fpChange = proteinNames[k].size() - tpChange;
if (trivialGrouping_) {
if (tpChange > 0) tpChange = 1;
if (fpChange > 0) fpChange = 1;
}
fdrCalculator.calcFDRs(fpChange, tpChange, prob, empq, estq);
}
if (kUpdateRocN) rocN_ = fdrCalculator.getRocN();
}
void FidoInterface::updateTargetDecoySizes() {
std::vector<std::vector<std::string> > proteinNames;
proteinGraph_->getProteinNames(proteinNames);
numberTargetProteins_ = 0;
numberDecoyProteins_ = 0;
for (unsigned int k = 0; k < proteinNames.size(); ++k) {
unsigned tpChange = countTargets(proteinNames[k]);
unsigned fpChange = proteinNames[k].size() - tpChange;
if (trivialGrouping_) {
if (tpChange > 0) numberTargetProteins_ += 1;
if (fpChange > 0) numberDecoyProteins_ += 1;
}
}
}
void FidoInterface::getROC_AUC(const std::vector<std::vector<string> > &names,
const std::vector<double> &probabilities, double &auc) {
/* Estimate ROC auc1 area as : (So - no(no + 1) / 2) / (no*n1)
* where no = number of target
* where n1 = number of decoy
* where So = SUM ri
* where ri is the rank of i target in the ranked list of target and decoys
*/
/* Estimate ROC auc2 area as : sum trapezoid area of each segment (integral of absolute value)
* A_segment(i) = abs(X1-Xo) * abs((y1 + y2 ) / 2)
* Where yo = number TP at segment i
* Where y1 = number TP at segment i + 1
* Where Xo = number FP at segment i
* Where X1 = number FP at segment i + 1
* Total Area = Total Area / total_TP * total_FP
*/
/* Estimate ROC auc3 area as : sum trapezoid area with antiderivatives of each segment (absolute value of the integral)
* A_segment(i) = ((yo - m*Xo)*X1 + m/2 * X1^2) - ((yo - m*Xo)*Xo - m/2 * X2^2))
* Where yo = number TP at segment i
* Where y1 = number TP at segment i + 1
* Where Xo = number FP at segment i
* Where X2 = number FP at segment i + 1
* Where m = (y1 - y0) / (X1 - X0)
* Total Area = abs(Total Area / total_TP * total_FP)
*/
std::vector<bool> ranked_list; // true if is decoy
std::vector<unsigned> tpArray,fpArray;
unsigned prev_tp,prev_fp,tp,fp;
prev_tp = prev_fp = tp = fp = 0;
double prev_prob = -1;
auc = 0.0;
// assuming names and probabilities same size; rocN_ set by getEstimated_and_Empirical_FDR()
for (unsigned k = 0; k < names.size() && fp <= rocN_; k++) {
double prob = probabilities[k];
unsigned tpChange = countTargets(names[k]);
unsigned fpChange = names[k].size() - tpChange;
//if ties activated count groups as 1 protein
if (trivialGrouping_) {
if (tpChange > 0) tpChange = 1;
if (fpChange > 0) fpChange = 1;
}
tp += tpChange;
fp += fpChange;
//should only do it when fp changes and either of them is != 0
if (prev_prob != -1 && fp != 0 && tp != 0 && fp != prev_fp) {
double trapezoid = trapezoid_area(fp,prev_fp,tp,prev_tp);
prev_fp = fp;
prev_tp = tp;
auc += trapezoid;
}
prev_prob = prob;
}
unsigned normalizer = (tp * fp);
if (normalizer > 0) {
auc /= normalizer;
} else {
auc = 0.0;
}
return;
}
void FidoInterface::getEstimated_and_Empirical_FDR(const std::vector<std::vector<string> > &names,
const std::vector<double> &probabilities,
std::vector<double> &empq,
std::vector<double> &estq)
{
empq.clear();
estq.clear();
double fpCount = 0.0, tpCount = 0.0;
double totalFDR = 0.0, estFDR = 0.0, empFDR = 0.0;
double TargetDecoyRatio = (double)numberTargetProteins / (double)numberDecoyProteins;
double previousEmpQ = 0.0;
double previousEstQ = 0.0;
if(updateRocN) rocN = 50;
//NOTE no need to store more q values since they will not be taken into account while estimating MSE FDR divergence
for (unsigned int k=0; (k<names.size() && (estFDR <= threshold)); k++)
{
double prob = probabilities[k];
if(tiesAsOneProtein)
{
unsigned tpChange = countTargets(names[k]);
unsigned fpChange = names[k].size() - tpChange;
fpCount += (double)fpChange;
tpCount += (double)tpChange;
if(countDecoyQvalue)
{
totalFDR += (prob) * (double)(tpChange + fpChange);
estFDR = totalFDR / (tpCount + fpCount);
}
else
{
totalFDR += (prob) * (double)(tpChange);
estFDR = totalFDR / (tpCount);
}
if(tpCount) empFDR = (fpCount * pi0 * TargetDecoyRatio) / tpCount;
if(empFDR > 1.0 || std::isnan(empFDR) || std::isinf(empFDR)) empFDR = 1.0;
if(estFDR > 1.0 || std::isnan(estFDR) || std::isinf(estFDR)) estFDR = 1.0;
if(estFDR < previousEstQ) estFDR = previousEstQ;
else previousEstQ = estFDR;
if(empFDR < previousEmpQ) empFDR = previousEmpQ;
else previousEmpQ = empFDR;
if(updateRocN)
{
rocN = (unsigned)std::max(rocN,(unsigned)std::max(50,std::min((int)fpCount,500)));
}
estq.push_back(estFDR);
empq.push_back(empFDR);
}
else
{
for(unsigned i=0; i<names[k].size(); i++)
{
std::string protein = names[k][i];
bool isdecoy = isDecoy(protein);
if(isdecoy)
{
fpCount++;
}
else
{
tpCount++;
}
if(countDecoyQvalue)
{
totalFDR += (prob);
estFDR = totalFDR / (tpCount + fpCount);
}
else if(tpCount)
{
if(!((bool)isdecoy)) totalFDR += (prob);
estFDR = totalFDR / (tpCount);
}
if(tpCount) empFDR = (fpCount * pi0 * TargetDecoyRatio) / tpCount;
if(empFDR > 1.0 || std::isnan(empFDR) || std::isinf(empFDR)) empFDR = 1.0;
if(estFDR > 1.0 || std::isnan(estFDR) || std::isinf(estFDR)) estFDR = 1.0;
if(estFDR < previousEstQ) estFDR = previousEstQ;
else previousEstQ = estFDR;
if(empFDR < previousEmpQ) empFDR = previousEmpQ;
else previousEmpQ = empFDR;
if(updateRocN)
{
rocN = (unsigned)std::max(rocN,(unsigned)std::max(50,std::min((int)fpCount,500)));
}
estq.push_back(estFDR);
empq.push_back(empFDR);
}
}
}
return;
}
