Package org.gorpipe.gor.gava

Class RegularLogLikelihood

java.lang.Object

org.gorpipe.gor.gava.GavaLogLikelihood

org.gorpipe.gor.gava.RegularLogLikelihood

public class RegularLogLikelihood
extends GavaLogLikelihood

Log likelihood calculator for regular variant association.

Field Summary

Fields inherited from class org.gorpipe.gor.gava.GavaLogLikelihood

casePenetrance, controlPenetrance, includeProtective, noMaxAlleleCounts, numCases, numControls, upperFreqThreshold

Constructor Summary

Constructors

Constructor	Description
RegularLogLikelihood()

Method Summary

Modifier and Type	Method	Description
double	computeLogLikelihood(java.util.List<org.gorpipe.gor.gava.CollapsedCounts> collapsedCounts, int[] perm, boolean debug)	Compute the log-likelihood ratio for a feature.

Methods inherited from class org.gorpipe.gor.gava.GavaLogLikelihood

calcVariantLogLikelihood, setIncludeProtective, setPenetrance, setSubjectCounts, setUpperFreqThreshold

Methods inherited from class java.lang.Object

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

Constructor Detail

RegularLogLikelihood

public RegularLogLikelihood()

Method Detail

computeLogLikelihood

public double computeLogLikelihood(java.util.List<org.gorpipe.gor.gava.CollapsedCounts> collapsedCounts,
                                   int[] perm,
                                   boolean debug)

Description copied from class: GavaLogLikelihood

Compute the log-likelihood ratio for a feature. The first numControls subjects in the given permutation are used as controls, and the remaining perm.length-numControls are used as cases.

Specified by:

computeLogLikelihood in class GavaLogLikelihood

Parameters:

collapsedCounts - the call counts for the subjects (with very rare variants collapsed)

perm - permutation of the subjects

debug - if true, print out debug information

Returns: