public static MixtureModel FitMixtureModel(IList <int> ad, IList <int> dp, double[] startingMeans)
{
var mm = new MixtureModel(ad, dp, startingMeans);
mm.FitBinomialModel();
return(mm);
}
public static MixtureModel UsePrefitModel(IList <int> ad, IList <int> dp, double[] means, double[] priors)
{
var mm = new MixtureModel(ad, dp, means, priors);
mm.UpdateClusteringAndQScore();
return(mm);
}
/// <summary>
/// Calculates the Q score and genotype posteriors of a 1/2 locus using a multinomial distribution.
/// This method is called from Pisces variant caller.
/// </summary>
/// <param name="allele1"></param>
/// <param name="allele2"></param>
/// <param name="models">IList of models for allele1 and allele 2. Each model is a 3 element double array.</param>
/// <returns>RecalibratedVariant that contains the Q score and genotype posteriors.</returns>
public static MixtureModelResult GetMultiAllelicQScores(CalledAllele allele1, CalledAllele allele2,
IList <double[]> models)
{
int totalCoverage = allele1.TotalCoverage;
int[] alleleDepths = new int[3];
alleleDepths[2] = allele2.AlleleSupport;
alleleDepths[1] = allele1.AlleleSupport;
// "Reference" here is not really reference--it is just everything else that was not the top two alleles
alleleDepths[0] = Math.Max(totalCoverage - alleleDepths[1] - alleleDepths[2], 0);
return(MixtureModel.GetMultinomialQScores(alleleDepths, totalCoverage, models));
}
/// <summary>
/// Calculates Q score of a called allele.
/// </summary>
/// <param name="allele"> Called allele from Pisces variant caller. </param>
/// <param name="model"> Means of binomial model to be used to estimate Q score. If this has more than three elements,
/// the elements closest to 0, 0.5 and 1 are used as the alleles true category. </param>
/// <param name="priors"> Prior probability for that category. The length must match the length of model. </param>
/// <returns> RecalibratedVariant that holds the Q scores and posteriors of the allele. </returns>
public static MixtureModelResult GetGenotypeAndQScore(CalledAllele allele, double[] model, double[] priors)
{
var(alleleSupport, totalDepth) = PreprocessCalledAllele(allele);
return(MixtureModel.CalculateQScoreAndGenotypePosteriors(alleleSupport, totalDepth, model, priors));
}
public static SimplifiedDiploidGenotype GetSimplifiedGenotype(CalledAllele allele, double[] model, double[] priors)
{
var(alleleSupport, totalDepth) = PreprocessCalledAllele(allele);
return(MixtureModel.GetSimplifiedGenotype(alleleSupport, totalDepth, model, priors));
}
