public double get_P_LN() {
double pLN = 0;
ChiSquaredDistribution chid = new ChiSquaredDistributionImpl(degree_freedom_wald);
try {
pLN = 1 - chid.cumulativeProbability(lod / 0.217);
} catch (Exception E) {
E.printStackTrace(System.err);
}
return pLN;
}
public void SummuarySimulation() {
calculatePower();
PrintStream Pout1 = null;
PrintStream Pout2 = null;
PrintStream Pout3 = null;
PrintStream Pout4 = null;
PrintStream Pout5 = null;
PrintStream Pout6 = null;
ChiSquaredDistribution chi = new ChiSquaredDistributionImpl(weight.length);
try {
Pout1 = new PrintStream(new BufferedOutputStream(new FileOutputStream("LogAP.txt")));
Pout2 = new PrintStream(new BufferedOutputStream(new FileOutputStream("LNP.txt")));
Pout3 = new PrintStream(new BufferedOutputStream(new FileOutputStream("LN.txt")));
Pout4 = new PrintStream(new BufferedOutputStream(new FileOutputStream("Wald.txt")));
Pout5 = new PrintStream(new BufferedOutputStream(new FileOutputStream("F.txt")));
Pout6 = new PrintStream(new BufferedOutputStream(new FileOutputStream("LogDP.txt")));
} catch (Exception E) {
E.printStackTrace(System.err);
}
for (int i = 0; i < SimulationResults.size(); i++) {
ArrayList PointStatistics = (ArrayList) SimulationResults.get(i);
double[] LRT = new double[PointStatistics.size()];
double[] WALD = new double[PointStatistics.size()];
DescriptiveStatistics dsLRT = new DescriptiveStatisticsImpl();
DescriptiveStatistics dsWALD = new DescriptiveStatisticsImpl();
SimpleRegression sr = new SimpleRegression();
for (int j = 0; j < PointStatistics.size(); j++) {
PointMappingStatistic pms = (PointMappingStatistic) PointStatistics.get(j);
double lod = pms.get_LOD() > 0 ? pms.get_LOD() : 0;
double ln = pms.get_LN();
double p = 0;
try {
p = chi.cumulativeProbability(ln);
} catch (Exception E) {
E.printStackTrace(System.err);
}
double logLOD = -1 * Math.log10(1 - p);
Pout1.print(pms.get_logP_additive() + " ");
Pout2.print(logLOD + " ");
Pout3.print(pms.get_LN() + " ");
Pout4.print(pms.get_wald() + " ");
Pout5.print(pms.get_logP_F() + " ");
Pout6.print(pms.get_logP_dominance() + " ");
dsLRT.addValue(pms.get_LN());
dsWALD.addValue(pms.get_wald());
LRT[j] = pms.get_LN();
WALD[j] = pms.get_wald();
sr.addData(pms.get_LN(), pms.get_wald());
}
System.out.println(
dsLRT.getMean()
+ " +- "
+ dsLRT.getStandardDeviation()
+ " "
+ dsWALD.getMean()
+ " +- "
+ dsWALD.getStandardDeviation()
+ " cor "
+ sr.getR());
dsLRT.clear();
dsWALD.clear();
sr.clear();
Pout1.println();
Pout2.println();
Pout3.println();
Pout4.println();
Pout5.println();
Pout6.println();
}
Pout1.close();
Pout2.close();
Pout3.close();
Pout4.close();
Pout5.close();
Pout6.close();
}
private void calculatePower() {
ChiSquaredDistribution chi = new ChiSquaredDistributionImpl(weight.length);
Collections.sort(thresholdAP);
Collections.sort(thresholdDP);
Collections.sort(thresholdLOD);
Collections.sort(thresholdPwald);
Collections.sort(thresholdPF);
EmpiricalLogBonAP =
((Double) thresholdAP.get((new Double((thresholdAP.size() - 1) * 0.95)).intValue()))
.doubleValue();
if (weight.length > 1) {
EmpiricalLogBonDP =
((Double) thresholdDP.get((new Double((thresholdDP.size() - 1) * 0.95)).intValue()))
.doubleValue();
}
threshold_LOD =
((Double) thresholdLOD.get((new Double((thresholdLOD.size() - 1) * 0.95)).intValue()))
.doubleValue();
threshold_lodp = 0;
double ln = threshold_LOD / 0.217;
threshold_Pwald =
((Double) thresholdPwald.get((new Double((thresholdPwald.size() - 1) * 0.95)).intValue()))
.doubleValue();
threshold_PF =
((Double) thresholdPF.get((new Double((thresholdPF.size() - 1) * 0.95)).intValue()))
.doubleValue();
try {
threshold_lodp = -1 * Math.log10(1 - chi.cumulativeProbability(ln));
} catch (Exception E) {
E.printStackTrace(System.err);
}
System.out.println("BonT: " + BonT);
System.out.println("LogBon: " + LogBon);
System.out.println("EmpLogBonAP: " + EmpiricalLogBonAP);
System.out.println("EmpLogBonDP: " + EmpiricalLogBonDP);
System.out.println(
"threshold_LOD: " + "log10:" + threshold_LOD + " LR: " + ln + " P(ln) " + threshold_lodp);
System.out.println("threshold_PWald: " + threshold_Pwald);
System.out.println("threshold_PF: " + threshold_PF);
for (Iterator e = SimulationResults.iterator(); e.hasNext(); ) {
ArrayList result = (ArrayList) e.next();
for (Iterator e1 = result.iterator(); e1.hasNext(); ) {
PointMappingStatistic pms = (PointMappingStatistic) e1.next();
String key = pms.getKey();
if (Param1.permutation > 0
&& pointPowerF.containsKey(key)
&& pms.get_logP_F() > threshold_PF) {
int p = ((Integer) pointPowerF.get(key)).intValue();
p++;
pointPowerF.put(key, new Integer(p));
}
if (Param1.permutation > 0
&& pointPowerWald.containsKey(key)
&& pms.get_logP_wald() > threshold_Pwald) {
int p = ((Integer) pointPowerWald.get(key)).intValue();
p++;
pointPowerWald.put(key, new Integer(p));
}
if (Param1.permutation > 0
&& pointPowerLOD.containsKey(key)
&& pms.get_LOD() > threshold_LOD) {
int p = ((Integer) pointPowerLOD.get(key)).intValue();
p++;
pointPowerLOD.put(key, new Integer(p));
}
if (pointPowerAPvalue.containsKey(key) && pms.get_logP_additive() > LogBon) {
int p = ((Integer) pointPowerAPvalue.get(key)).intValue();
p++;
pointPowerAPvalue.put(key, new Integer(p));
}
if (pointPowerEmpiricalAPvalue.containsKey(key)
&& pms.get_logP_additive() > EmpiricalLogBonAP) {
int p = ((Integer) pointPowerEmpiricalAPvalue.get(key)).intValue();
p++;
pointPowerEmpiricalAPvalue.put(key, new Integer(p));
}
if (weight.length > 1) {
if (pointPowerDPvalue.containsKey(key) && pms.get_logP_dominance() > LogBon) {
int p = ((Integer) pointPowerDPvalue.get(key)).intValue();
p++;
pointPowerDPvalue.put(key, new Integer(p));
}
if (pointPowerEmpiricalDPvalue.containsKey(key)
&& pms.get_logP_dominance() > EmpiricalLogBonDP) {
int p = ((Integer) pointPowerEmpiricalDPvalue.get(key)).intValue();
p++;
pointPowerEmpiricalDPvalue.put(key, new Integer(p));
}
}
}
}
Set keys = pointPowerLOD.keySet();
System.out.println("type I LogBon: " + typeI_LogBon / Param1.permutation);
System.out.println("QTL\tFP\tWald\tLOD\tBonAP\tEmpAP\tBonDP\tEmpDP");
for (Iterator e = keys.iterator(); e.hasNext(); ) {
String key = (String) e.next();
System.out.print(key + "\t");
System.out.print((Integer) pointPowerF.get(key) + "\t");
System.out.print((Integer) pointPowerWald.get(key) + "\t");
System.out.print((Integer) pointPowerLOD.get(key) + "\t");
System.out.print((Integer) pointPowerAPvalue.get(key) + "\t");
System.out.print((Integer) pointPowerEmpiricalAPvalue.get(key) + "\t");
if (weight.length > 1) {
System.out.print(pointPowerDPvalue.get(key) + "\t");
System.out.println(pointPowerEmpiricalDPvalue.get(key) + "\t");
} else {
System.out.println("--\t--\t");
}
}
}
/**
* @param param degrees of freedom
* @return chi squared distribution
*/
protected ChiSquaredDistribution getChiSquaredDistribution(double param) {
if (chisquared == null || chisquared.getDegreesOfFreedom() != param)
chisquared = new ChiSquaredDistributionImpl(param);
return chisquared;
}
