org.broadinstitute.hellbender.tools.walkers.mutect

Class SomaticLikelihoodsEngine

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine

public class SomaticLikelihoodsEngine
extends java.lang.Object

Created by David Benjamin on 3/9/17.

Field Summary

Fields

Modifier and Type	Field and Description
static double	CONVERGENCE_THRESHOLD

Constructor Summary

Constructors

Constructor and Description
SomaticLikelihoodsEngine()

Method Summary

Modifier and Type	Method and Description
static double[]	alleleFractionsPosterior(org.apache.commons.math3.linear.RealMatrix logLikelihoods, double[] priorPseudocounts) Given a likelihoods matrix, calculate the parameters of the Dirichlet posterior distribution on their allele fractions, which define a discrete distribution.
protected static double[]	getEffectiveCounts(org.apache.commons.math3.linear.RealMatrix logLikelihoods, double[] dirichletPrior) Given data log likelihoods and a Dirichlet prior for a categorical distribution, obtain the array of total responsibilities for each category
static double	logDirichletNormalization(double... dirichletParams)
static double	logEvidence(org.apache.commons.math3.linear.RealMatrix logLikelihoods, double[] priorPseudocounts)
static double	logEvidence(org.apache.commons.math3.linear.RealMatrix logLikelihoods, double[] priorPseudocounts, double alleleFractionThreshold, int nonRefIndex)
static double	logEvidence(org.apache.commons.math3.linear.RealMatrix logLikelihoods, double minAF, int nonRefIndex)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

CONVERGENCE_THRESHOLD

public static final double CONVERGENCE_THRESHOLD

See Also:

Constant Field Values

Constructor Detail

SomaticLikelihoodsEngine

public SomaticLikelihoodsEngine()

Method Detail

alleleFractionsPosterior

public static double[] alleleFractionsPosterior(org.apache.commons.math3.linear.RealMatrix logLikelihoods,
                                                double[] priorPseudocounts)

Given a likelihoods matrix, calculate the parameters of the Dirichlet posterior distribution on their allele fractions, which define a discrete distribution.

Parameters:

logLikelihoods - matrix of alleles x reads

priorPseudocounts -

getEffectiveCounts

protected static double[] getEffectiveCounts(org.apache.commons.math3.linear.RealMatrix logLikelihoods,
                                             double[] dirichletPrior)

Given data log likelihoods and a Dirichlet prior for a categorical distribution, obtain the array of total responsibilities for each category

Parameters:

logLikelihoods -

dirichletPrior -

Returns:

logEvidence

public static double logEvidence(org.apache.commons.math3.linear.RealMatrix logLikelihoods,
                                 double[] priorPseudocounts)

Parameters:

logLikelihoods - matrix of alleles x reads

priorPseudocounts -

logEvidence

public static double logEvidence(org.apache.commons.math3.linear.RealMatrix logLikelihoods,
                                 double[] priorPseudocounts,
                                 double alleleFractionThreshold,
                                 int nonRefIndex)

Parameters:

logLikelihoods - matrix of alleles x reads (NOTE: NON_REF allele is assumed to be last)

priorPseudocounts -

alleleFractionThreshold - lower bound of allele fractions to consider for non-ref likelihood

logEvidence

public static double logEvidence(org.apache.commons.math3.linear.RealMatrix logLikelihoods,
                                 double minAF,
                                 int nonRefIndex)

logDirichletNormalization

public static double logDirichletNormalization(double... dirichletParams)