private void convertResultsToPValues(WorkPackage wp, Result dsResults) {
// per probe, convert to p-value
int numProbes = dsResults.zscores[0].length;
boolean hasResults = false;
for (int p = 0; p < numProbes; p++) {
int nrDatasetsPassingQC = 0;
int nrTotalSamples = 0;
double zSum = 0;
double betasum = 0;
for (int d = 0; d < m_numDatasets; d++) {
// TODO: check whether this actually returns the correct Z-scores: should the stored values
// be flipped?
double zscore = dsResults.zscores[d][p];
double correlation = dsResults.correlations[d][p];
Integer numSamples = dsResults.numSamples[d];
if (!Double.isNaN(correlation)) {
boolean flipalleles = wp.getFlipSNPAlleles()[d];
if (m_useAbsoluteZScores) {
zscore = Math.abs(zscore);
dsResults.zscores[d][p] = Math.abs(zscore);
dsResults.correlations[d][p] = Math.abs(correlation);
if (!Double.isNaN(dsResults.beta[d][p])) {
dsResults.beta[d][p] = Math.abs(dsResults.beta[d][p]);
}
wp.getFlipSNPAlleles()[d] = false;
} else if (flipalleles) {
zscore = -zscore;
// dsResults.zscores[d][p] = zscore;
// correlation = -correlation;
// dsResults.correlations[d][p] = correlation;
}
nrDatasetsPassingQC++;
double weight = Descriptives.getSqrt(numSamples);
zSum += (zscore * weight);
nrTotalSamples += numSamples;
if (determinebeta) {
if (flipalleles) {
betasum += (-dsResults.beta[d][p] * numSamples);
dsResults.beta[d][p] = -dsResults.beta[d][p];
} else {
betasum += (dsResults.beta[d][p] * numSamples);
}
}
}
}
if (nrTotalSamples > 0
&& (testSNPsPresentInBothDatasets && nrDatasetsPassingQC == m_numDatasets)
|| (!testSNPsPresentInBothDatasets && nrDatasetsPassingQC > 0)) {
testsPerformed++;
hasResults = true;
double sqrtSample = Descriptives.getSqrt(nrTotalSamples);
double zScore = zSum / sqrtSample;
double pValueOverall = Descriptives.convertZscoreToPvalue(zScore);
dsResults.pvalues[p] = pValueOverall;
dsResults.finalZScore[p] = zScore;
// determine assessed allele....
if (determinebeta) {
betasum /= nrTotalSamples;
double metase = 1 / Math.sqrt(nrTotalSamples);
dsResults.finalBeta[p] = betasum;
dsResults.finalBetaSe[p] = metase;
}
} else {
dsResults.pvalues[p] = Double.NaN;
dsResults.finalZScore[p] = Double.NaN;
}
}
wp.setHasResults(hasResults);
wp.setResult(dsResults);
}
