public void TestGetGtLogLikelihoodScore()
{
var copyNumberModelFactory = new HaplotypeCopyNumberModelFactory();
var copyNumberModel = copyNumberModelFactory.CreateModel(numCnStates: 5, maxCoverage: 200,
meanCoverage: 100, diploidAlleleMeanCounts: 50.0);
var simulatedCn = 3;
var gtModelCounts = PedigreeInfo.GeneratePhasedGenotype(numCnStates: 5).Where(gt => gt.TotalCopyNumber == simulatedCn)
.Select(gt => gt.PhasedGenotype).ToList();
var gtObservedCounts = new Balleles(new List <Ballele>
{
new Ballele(1, 1, 73),
new Ballele(100, 2, 74),
new Ballele(200, 1, 76),
new Ballele(300, 0, 74),
new Ballele(400, 1, 75),
new Ballele(500, 2, 74)
});
var gt0_3 = new PhasedGenotype(3, 0);
int?selectedGtState = null;
// variant caller only calls MCC, only upper triangle of CN genotypes is selected - i.e. CNa=3,CNb=0 from [CNa=3,CNb=0,CNa=0,CNb=3]
double logLikelihoodScore =
VariantCaller.GetGtLogLikelihoodScore(gtObservedCounts, gtModelCounts, ref selectedGtState,
copyNumberModel);
Assert.Equal(gtModelCounts.IndexOf(gt0_3), selectedGtState);
gtObservedCounts = new Balleles(new List <Ballele>
{
new Ballele(1, 23, 53),
new Ballele(100, 22, 54),
new Ballele(200, 25, 46),
new Ballele(300, 24, 50),
new Ballele(400, 26, 51),
new Ballele(500, 24, 51)
});
var gt1_2 = new PhasedGenotype(2, 1);
selectedGtState = null;
// variant caller only calls MCC, only upper triangle of CN genotypes is selected - i.e. CNa=3,CNb=0 from [CNa=3,CNb=0,CNa=0,CNb=3]
logLikelihoodScore =
VariantCaller.GetGtLogLikelihoodScore(gtObservedCounts, gtModelCounts, ref selectedGtState,
copyNumberModel);
Assert.Equal(gtModelCounts.IndexOf(gt1_2), selectedGtState);
}
public void HaplotypeCopyNumberModelTester_Gain_CN4()
{
var copyNumberModelFactory = new HaplotypeCopyNumberModelFactory();
var copyNumberModel = copyNumberModelFactory.CreateModel(numCnStates: 5, maxCoverage: 300, meanCoverage: 100, diploidAlleleMeanCounts: 50.0);
var bAlleles = new Balleles(new List <Ballele>
{
new Ballele(1, 200, 1),
new Ballele(100, 202, 2),
new Ballele(200, 209, 3),
new Ballele(300, 1, 198),
new Ballele(400, 201, 2),
new Ballele(500, 199, 1)
});
double gt40 = copyNumberModel.GetGenotypeLogLikelihood(bAlleles, new PhasedGenotype(4, 0));
double gt31 = copyNumberModel.GetGenotypeLogLikelihood(bAlleles, new PhasedGenotype(3, 1));
double gt04 = copyNumberModel.GetGenotypeLogLikelihood(bAlleles, new PhasedGenotype(0, 4));
Assert.True(gt40 > gt31);
Assert.True(gt40 == gt04);
}
public void HaplotypeCopyNumberModelTester_HetLoss()
{
var copyNumberModelFactory = new HaplotypeCopyNumberModelFactory();
var copyNumberModel = copyNumberModelFactory.CreateModel(numCnStates: 5, maxCoverage: 200, meanCoverage: 100, diploidAlleleMeanCounts: 50.0);
var bAlleles = new Balleles(new List <Ballele>
{
new Ballele(1, 31, 1),
new Ballele(100, 39, 2),
new Ballele(200, 33, 3),
new Ballele(300, 1, 33),
new Ballele(400, 36, 2),
new Ballele(500, 27, 1)
});
double gt10 = copyNumberModel.GetGenotypeLogLikelihood(bAlleles, new PhasedGenotype(1, 0));
double gt20 = copyNumberModel.GetGenotypeLogLikelihood(bAlleles, new PhasedGenotype(2, 0));
double gt01 = copyNumberModel.GetGenotypeLogLikelihood(bAlleles, new PhasedGenotype(0, 1));
Assert.True(gt10 > gt20);
Assert.True(gt10 == gt01);
}
public void HaplotypeCopyNumberModelTester_PhasedGenotype_LossOfHeterozygosity()
{
var copyNumberModelFactory = new HaplotypeCopyNumberModelFactory();
var copyNumberModel = copyNumberModelFactory.CreateModel(numCnStates: 5, maxCoverage: 200, meanCoverage: 100, diploidAlleleMeanCounts: 50.0);
var bAlleles = new Balleles(new List <Ballele>
{
new Ballele(1, 50, 1),
new Ballele(100, 25, 24),
new Ballele(200, 23, 27),
new Ballele(300, 25, 24),
new Ballele(400, 1, 50),
new Ballele(500, 25, 25)
});
double diploidHet = copyNumberModel.GetGenotypeLogLikelihood(bAlleles, new PhasedGenotype(1, 1));
double lohB = copyNumberModel.GetGenotypeLogLikelihood(bAlleles, new PhasedGenotype(0, 2));
double lohA = copyNumberModel.GetGenotypeLogLikelihood(bAlleles, new PhasedGenotype(2, 0));
Assert.True(diploidHet > lohB);
Assert.True(diploidHet > lohA);
var bAllelesLohWithNoise = new Balleles(new List <Ballele>
{
new Ballele(1, 53, 1),
new Ballele(100, 50, 1),
new Ballele(200, 47, 2),
new Ballele(300, 46, 0),
new Ballele(400, 48, 2),
new Ballele(500, 53, 0)
});
diploidHet = copyNumberModel.GetGenotypeLogLikelihood(bAllelesLohWithNoise, new PhasedGenotype(1, 1));
lohB = copyNumberModel.GetGenotypeLogLikelihood(bAllelesLohWithNoise, new PhasedGenotype(0, 2));
lohA = copyNumberModel.GetGenotypeLogLikelihood(bAllelesLohWithNoise, new PhasedGenotype(2, 0));
Assert.True(diploidHet < lohB);
Assert.True(diploidHet < lohA);
}
