Package org.gorpipe.gor.gava

Class GavaLogLikelihood

java.lang.Object

org.gorpipe.gor.gava.GavaLogLikelihood

Direct Known Subclasses:

DominantLogLikelihood, RecessiveLogLikelihood, RegularLogLikelihood

public abstract class GavaLogLikelihood
extends Object

Log-likelihood ratio calculator for variant association.

Field Summary

Fields

Modifier and Type	Field	Description
protected int	casePenetrance	Case penetrance (0 for no locus hetreogeneity, -1 for no constraint).
protected int	controlPenetrance	Control penetrance (0 for complete penetrance, -1 for no constraint).
protected boolean	includeProtective	Include protective variants in calculations.
protected boolean	noMaxAlleleCounts	No max allele count for each case in dominant/recessive models.
protected int	numCases
protected int	numControls
protected double	upperFreqThreshold	Upper threshold for the control allele frequency.

Constructor Summary

Constructors

Constructor	Description
GavaLogLikelihood()

Method Summary

Modifier and Type	Method	Description
double	calcVariantLogLikelihood(VariantCounts counts, int[] perm)	Calculate the log-likelihood for a single variant (using the regular inheritance model).
abstract double	computeLogLikelihood(List<org.gorpipe.gor.gava.CollapsedCounts> collapsedCounts, int[] perm, boolean debug)	Compute the log-likelihood ratio for a feature.
void	setIncludeProtective(boolean includeProtective)	Set if protective variants should be included (default is false).
void	setPenetrance(int controlPenetrance, int casePenetrance, boolean noMaxAlleleCounts)
void	setSubjectCounts(int numCases, int numControls)
void	setUpperFreqThreshold(double upperFreqThreshold)

Methods inherited from class java.lang.Object

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

Field Details

upperFreqThreshold

protected double upperFreqThreshold

Upper threshold for the control allele frequency.

controlPenetrance

protected int controlPenetrance

Control penetrance (0 for complete penetrance, -1 for no constraint).

casePenetrance

protected int casePenetrance

Case penetrance (0 for no locus hetreogeneity, -1 for no constraint).

noMaxAlleleCounts

protected boolean noMaxAlleleCounts

No max allele count for each case in dominant/recessive models.

includeProtective

protected boolean includeProtective

Include protective variants in calculations.

numCases

protected int numCases

numControls

protected int numControls

Constructor Details

GavaLogLikelihood

public GavaLogLikelihood()

Method Details

setSubjectCounts

public void setSubjectCounts(int numCases,
 int numControls)

Parameters:

numCases -

numControls -

setPenetrance

public void setPenetrance(int controlPenetrance,
 int casePenetrance,
 boolean noMaxAlleleCounts)

Parameters:

controlPenetrance - maximum count among controls, -1 for no constraint

casePenetrance - true if recessive/dominant with no locus heterogeneity

noMaxAlleleCounts - true if no max allele count for each case in dominant/recessive models

setUpperFreqThreshold

public void setUpperFreqThreshold(double upperFreqThreshold)

Parameters:

upperFreqThreshold - upper threshold for the allele frequency

setIncludeProtective

public void setIncludeProtective(boolean includeProtective)

Set if protective variants should be included (default is false).

Parameters:

includeProtective - true to include protective variants, false to exclude

computeLogLikelihood

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

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.

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:

the log-likelihood

calcVariantLogLikelihood

public double calcVariantLogLikelihood(VariantCounts counts,
 int[] perm)

Calculate the log-likelihood for a single variant (using the regular inheritance model).

Parameters:

counts - the call counts for the variant

perm - permutation of the subjects

Returns:

the log-likelihood