org.broadinstitute.hellbender.tools.copynumber.arguments

Class SomaticSegmentationArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection

All Implemented Interfaces:

java.io.Serializable

public class SomaticSegmentationArgumentCollection
extends java.lang.Object
implements java.io.Serializable

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Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	KERNEL_APPROXIMATION_DIMENSION_LONG_NAME
static java.lang.String	KERNEL_SCALING_ALLELE_FRACTION_LONG_NAME
static java.lang.String	KERNEL_VARIANCE_ALLELE_FRACTION_LONG_NAME
static java.lang.String	KERNEL_VARIANCE_COPY_RATIO_LONG_NAME
int	kernelApproximationDimension
double	kernelScalingAlleleFraction
double	kernelVarianceAlleleFraction
double	kernelVarianceCopyRatio
static java.lang.String	MAXIMUM_NUMBER_OF_SEGMENTS_PER_CHROMOSOME_LONG_NAME
int	maxNumSegmentsPerChromosome
static java.lang.String	NUMBER_OF_CHANGEPOINTS_PENALTY_FACTOR_LONG_NAME
double	numChangepointsPenaltyFactor
static long	serialVersionUID
static java.lang.String	WINDOW_SIZE_LONG_NAME
java.util.List<java.lang.Integer>	windowSizes

Constructor Summary

Constructors

Constructor and Description
SomaticSegmentationArgumentCollection()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

serialVersionUID

public static final long serialVersionUID

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Constant Field Values

MAXIMUM_NUMBER_OF_SEGMENTS_PER_CHROMOSOME_LONG_NAME

public static final java.lang.String MAXIMUM_NUMBER_OF_SEGMENTS_PER_CHROMOSOME_LONG_NAME

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Constant Field Values

KERNEL_VARIANCE_COPY_RATIO_LONG_NAME

public static final java.lang.String KERNEL_VARIANCE_COPY_RATIO_LONG_NAME

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Constant Field Values

KERNEL_VARIANCE_ALLELE_FRACTION_LONG_NAME

public static final java.lang.String KERNEL_VARIANCE_ALLELE_FRACTION_LONG_NAME

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Constant Field Values

KERNEL_SCALING_ALLELE_FRACTION_LONG_NAME

public static final java.lang.String KERNEL_SCALING_ALLELE_FRACTION_LONG_NAME

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Constant Field Values

KERNEL_APPROXIMATION_DIMENSION_LONG_NAME

public static final java.lang.String KERNEL_APPROXIMATION_DIMENSION_LONG_NAME

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Constant Field Values

WINDOW_SIZE_LONG_NAME

public static final java.lang.String WINDOW_SIZE_LONG_NAME

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Constant Field Values

NUMBER_OF_CHANGEPOINTS_PENALTY_FACTOR_LONG_NAME

public static final java.lang.String NUMBER_OF_CHANGEPOINTS_PENALTY_FACTOR_LONG_NAME

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Constant Field Values

maxNumSegmentsPerChromosome

@Argument(doc="Maximum number of segments allowed per chromosome.",
          fullName="maximum-number-of-segments-per-chromosome",
          minValue=1.0,
          optional=true)
public int maxNumSegmentsPerChromosome

kernelVarianceCopyRatio

@Argument(doc="Variance of Gaussian kernel for copy-ratio segmentation, if performed.  If zero, a linear kernel will be used.",
          fullName="kernel-variance-copy-ratio",
          minValue=0.0,
          optional=true)
public double kernelVarianceCopyRatio

kernelVarianceAlleleFraction

@Argument(doc="Variance of Gaussian kernel for allele-fraction segmentation, if performed.  If zero, a linear kernel will be used.",
          fullName="kernel-variance-allele-fraction",
          minValue=0.0,
          optional=true)
public double kernelVarianceAlleleFraction

kernelScalingAlleleFraction

@Argument(doc="Relative scaling S of the kernel K_AF for allele-fraction segmentation to the kernel K_CR for copy-ratio segmentation.  If multidimensional segmentation is performed, the total kernel used will be K_CR + S * K_AF.",
          fullName="kernel-scaling-allele-fraction",
          minValue=0.0,
          optional=true)
public double kernelScalingAlleleFraction

kernelApproximationDimension

@Argument(doc="Dimension of the kernel approximation.  A subsample containing this number of data points will be used to construct the approximation for each chromosome.  If the total number of data points in a chromosome is greater than this number, then all data points in the chromosome will be used.  Time complexity scales quadratically and space complexity scales linearly with this parameter.",
          fullName="kernel-approximation-dimension",
          minValue=1.0,
          optional=true)
public int kernelApproximationDimension

windowSizes

@Argument(doc="Window sizes to use for calculating local changepoint costs.  For each window size, the cost for each data point to be a changepoint will be calculated assuming that the point demarcates two adjacent segments of that size.  Including small (large) window sizes will increase sensitivity to small (large) events.  Duplicate values will be ignored.",
          fullName="window-size",
          minValue=1.0,
          optional=true)
public java.util.List<java.lang.Integer> windowSizes

numChangepointsPenaltyFactor

@Argument(doc="Factor A for the penalty on the number of changepoints per chromosome for segmentation.  Adds a penalty of the form A * C * [1 + log (N / C)], where C is the number of changepoints in the chromosome and N is the number of data points in the chromosome, to the cost function for each chromosome.  Must be non-negative.",
          fullName="number-of-changepoints-penalty-factor",
          minValue=0.0,
          optional=true)
public double numChangepointsPenaltyFactor

Constructor Detail

SomaticSegmentationArgumentCollection

public SomaticSegmentationArgumentCollection()