org.broadinstitute.hellbender.tools.copynumber.denoising

Class SVDDenoisedCopyRatioResult

java.lang.Object

org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisedCopyRatioResult

public final class SVDDenoisedCopyRatioResult
extends java.lang.Object

Represents copy ratios for a sample that has been standardized and denoised by an SVDReadCountPanelOfNormals.

Constructor Summary

Constructors

Constructor and Description
SVDDenoisedCopyRatioResult(SampleLocatableMetadata metadata, java.util.List<SimpleInterval> intervals, org.apache.commons.math3.linear.RealMatrix standardizedCopyRatioValues, org.apache.commons.math3.linear.RealMatrix denoisedCopyRatioValues)

Method Summary

Modifier and Type	Method and Description
CopyRatioCollection	getDenoisedCopyRatios()
CopyRatioCollection	getStandardizedCopyRatios()
void	write(java.io.File standardizedCopyRatiosFile, java.io.File denoisedCopyRatiosFile)

Methods inherited from class java.lang.Object

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

Constructor Detail

SVDDenoisedCopyRatioResult

public SVDDenoisedCopyRatioResult(SampleLocatableMetadata metadata,
                                  java.util.List<SimpleInterval> intervals,
                                  org.apache.commons.math3.linear.RealMatrix standardizedCopyRatioValues,
                                  org.apache.commons.math3.linear.RealMatrix denoisedCopyRatioValues)

Method Detail

getStandardizedCopyRatios

public CopyRatioCollection getStandardizedCopyRatios()

getDenoisedCopyRatios

public CopyRatioCollection getDenoisedCopyRatios()

write

public void write(java.io.File standardizedCopyRatiosFile,
                  java.io.File denoisedCopyRatiosFile)