org.broadinstitute.hellbender.tools.copynumber.segmentation

Class AlleleFractionKernelSegmenter

java.lang.Object

org.broadinstitute.hellbender.tools.copynumber.segmentation.AlleleFractionKernelSegmenter

public final class AlleleFractionKernelSegmenter
extends java.lang.Object

Segments alternate-allele-fraction data using kernel segmentation. Segments do not span chromosomes.

Constructor Summary

Constructors

Constructor and Description
AlleleFractionKernelSegmenter(AllelicCountCollection allelicCounts)

Method Summary

Modifier and Type	Method and Description
AlleleFractionSegmentCollection	findSegmentation(int maxNumChangepointsPerChromosome, double kernelVariance, int kernelApproximationDimension, java.util.List<java.lang.Integer> windowSizes, double numChangepointsPenaltyLinearFactor, double numChangepointsPenaltyLogLinearFactor) Segments the internally held AllelicCountCollection using a separate KernelSegmenter for each chromosome.

Methods inherited from class java.lang.Object

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

Constructor Detail

AlleleFractionKernelSegmenter

public AlleleFractionKernelSegmenter(AllelicCountCollection allelicCounts)

Method Detail

findSegmentation

public AlleleFractionSegmentCollection findSegmentation(int maxNumChangepointsPerChromosome,
                                                        double kernelVariance,
                                                        int kernelApproximationDimension,
                                                        java.util.List<java.lang.Integer> windowSizes,
                                                        double numChangepointsPenaltyLinearFactor,
                                                        double numChangepointsPenaltyLogLinearFactor)

Segments the internally held AllelicCountCollection using a separate KernelSegmenter for each chromosome.

Parameters:

kernelVariance - variance of the Gaussian kernel; if zero, a linear kernel is used instead