Package org.broadinstitute.hellbender.tools.copynumber.denoising

Class SVDDenoisingUtils

java.lang.Object

org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisingUtils

public final class SVDDenoisingUtils
extends Object

Utility class for package-private methods for performing SVD-based denoising and related operations. These methods are specifically tailored for the SVD-denoising methods used in the GATK CNV pipeline and are not intended for wide reuse.

Method Summary

Modifier and Type	Method	Description
static org.apache.commons.math3.linear.RealMatrix	preprocessAndStandardizeSample(double[] readCounts, double[] intervalGCContent)	Preprocess (i.e., transform to fractional coverage and correct GC bias) and standardize read counts for samples when no panel of normals is available.

Methods inherited from class java.lang.Object

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

Method Details

preprocessAndStandardizeSample

public static org.apache.commons.math3.linear.RealMatrix preprocessAndStandardizeSample(double[] readCounts,
 double[] intervalGCContent)

Preprocess (i.e., transform to fractional coverage and correct GC bias) and standardize read counts for samples when no panel of normals is available. The original readCounts has dimensions 1 x intervals and is not modified. If intervalGCContent is null, GC-bias correction will not be performed