public void testBinomialCoefficient()
{
int n = 10;
int k = 2;
Assert.AreEqual(45, (int)GoTermNumber.binomialCoefficient(n, k));
}
public void testGoTerm_pValue()
{
int q = 2; //count of proteins in selected subset with the particular Go term
int k = 4; //count of proteins in selected subset
int m = 4; //count of proteins in background with the particular Go term
int t = 10; //count of proteins in background
Assert.AreEqual(0.54762, Math.Round((double)GoTermNumber.GoTerm_pValue(q, k, m, t), 5));
}
public void saveall()
{
SaveState.lollipop = new Lollipop();
ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("asdf");
SaveState.lollipop.qVals.Add(e.quant);
GoTermNumber g = new GoTermNumber(new GoTerm("id", "desc", Aspect.BiologicalProcess), 0, 0, 0, 0);
g.by = -1;
SaveState.lollipop.goTermNumbers.Add(g);
ResultsSummaryGenerator.save_all(TestContext.CurrentContext.TestDirectory, SaveState.time_stamp());
}
public void saveall()
{
Sweet.lollipop = new Lollipop();
ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("asdf");
Sweet.lollipop.qVals.Add(e.quant);
GoTermNumber g = new GoTermNumber(new GoTerm("id", "desc", Aspect.BiologicalProcess), 0, 0, 0, 0);
g.by = -1;
Sweet.lollipop.TusherAnalysis1.GoAnalysis.goTermNumbers.Add(g);
Sweet.lollipop.topdown_proteoforms = new List <TopDownProteoform>()
{
ConstructorsForTesting.TopDownProteoform("td1", 1000, 10)
};
ResultsSummaryGenerator.save_all(TestContext.CurrentContext.TestDirectory, Sweet.time_stamp(), Sweet.lollipop.TusherAnalysis1 as IGoAnalysis, Sweet.lollipop.TusherAnalysis1 as TusherAnalysis);
}
public void testLogOddsRatio()
{
int q = 1; // number of enriched proteins with the term
int k = 2; // number of enriched proteins
int m = 2; // number of proteins in the background with the term
int t = 4; // number of proteins in the background
DatabaseReference d = new DatabaseReference("GO", ":1", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:one")
});
GoTerm g = new GoTerm(d);
GoTermNumber gtn = new GoTermNumber(g, q, k, m, t);
Assert.AreEqual(0, gtn.log_odds_ratio);
//Assert.AreEqual(0.833333m, Math.Round((decimal)gtn.p_value.Truncate(7), 6));
Assert.AreEqual(0.833333m, Math.Round(gtn.p_value, 6));
q = 1; // number of enriched proteins with the term
k = 2; // number of enriched proteins
m = 4; // number of proteins in the background with the term
t = 4; // number of proteins in the background
gtn = new GoTermNumber(g, q, k, m, t);
Assert.AreEqual(-1, gtn.log_odds_ratio);
//Assert.AreEqual(1m, Math.Round((decimal)gtn.p_value.Truncate(7), 6));
Assert.AreEqual(1m, Math.Round(gtn.p_value, 6));
q = 2; // number of enriched proteins with the term
k = 2; // number of enriched proteins
m = 2; // number of proteins in the background with the term
t = 4; // number of proteins in the background
gtn = new GoTermNumber(g, q, k, m, t);
Assert.AreEqual(1, gtn.log_odds_ratio);
//Assert.AreEqual(0.166667m, Math.Round((decimal)gtn.p_value.Truncate(7), 6));
Assert.AreEqual(0.166667m, Math.Round(gtn.p_value, 6));
}
public DisplayGoTermNumber(GoTermNumber g)
: base(g)
{
gtn = g;
}
