public void BinaryContingencyNullTest()
{
BinaryContingencyTable e0 = CreateExperiment(0.25, 0.33, 0.33, 200);
Assert.IsTrue(e0.Total == 200);
Assert.IsTrue(e0.RowTotal(0) + e0.RowTotal(1) == e0.Total);
Assert.IsTrue(e0.ColumnTotal(0) + e0.ColumnTotal(1) == e0.Total);
UncertainValue lnr = e0.LogOddsRatio;
Assert.IsTrue(lnr.ConfidenceInterval(0.95).ClosedContains(0.0));
UncertainValue r = e0.OddsRatio;
Assert.IsTrue(r.ConfidenceInterval(0.95).ClosedContains(1.0));
TestResult f = e0.FisherExactTest();
Assert.IsTrue(f.RightProbability < 0.95, f.RightProbability.ToString());
}
public void BinaryContingencyTest()
{
BinaryContingencyTable e1 = CreateExperiment(0.50, 0.50, 0.75, 200);
Assert.IsTrue(e1.RowTotal(0) + e1.RowTotal(1) == e1.Total);
Assert.IsTrue(e1.ColumnTotal(0) + e1.ColumnTotal(1) == e1.Total);
UncertainValue lnr = e1.LogOddsRatio;
Assert.IsFalse(lnr.ConfidenceInterval(0.95).ClosedContains(0.0));
UncertainValue r = e1.OddsRatio;
Assert.IsFalse(r.ConfidenceInterval(0.95).ClosedContains(1.0));
TestResult p = e1.PearsonChiSquaredTest();
Assert.IsTrue(p.LeftProbability > 0.95, p.RightProbability.ToString());
TestResult f = e1.FisherExactTest();
Assert.IsTrue(f.RightProbability > 0.95);
}
private Dictionary <string, double> FisherExactTest(Dictionary <string, int> background, Dictionary <string, int> test)
{
Dictionary <string, double> pvalueDict = new Dictionary <string, double>();
int totalBackground = background.Values.Sum();
int totalTest = test.Values.Sum();
foreach (KeyValuePair <string, int> kvp in test)
{
int backgroundCount = background[kvp.Key];
int testCount = kvp.Value;
BinaryContingencyTable table = new BinaryContingencyTable();
//I got this from Doug's code. I hope it is right.
int upperleft = testCount;
int upperright = backgroundCount - upperleft;
int lowerleft = totalTest - upperleft;
int lowerright = totalBackground - totalTest - upperright;
table[0, 0] = upperleft;
table[0, 1] = upperright;
table[1, 0] = lowerleft;
table[1, 1] = lowerright;
TestResult fisherExactResult = table.FisherExactTest();
double pvalueLeft = fisherExactResult.LeftProbability;
double pvalueRight = fisherExactResult.LeftProbability;
pvalueDict.Add(kvp.Key, pvalueRight);
}
Dictionary <string, double> qvalueDict = BenjaminiHochberg(pvalueDict);
return(qvalueDict);
}