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; }