Package ubic.gemma.model.analysis.expression.diff

Class ContrastResult

java.lang.Object

ubic.gemma.model.analysis.expression.diff.ContrastResult

All Implemented Interfaces:

Serializable, Identifiable

public class ContrastResult
extends Object
implements Identifiable, Serializable

Represents a contrast between "conditions". In practice, this is the comparison between a factor level and the baseline; for interactions it is the difference of comparisons.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ContrastResult.Factory

Constructor Summary

Constructors

Constructor	Description
ContrastResult()

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object object)
Double	getCoefficient()
FactorValue	getFactorValue()
Long	getId()
Double	getLogFoldChange()
Double	getPvalue()
FactorValue	getSecondFactorValue()
Double	getTstat()
int	hashCode()
void	setCoefficient(Double coefficient)
void	setFactorValue(FactorValue factorValue)
void	setId(Long id)
void	setLogFoldChange(Double logFoldChange)
void	setPvalue(Double pvalue)
void	setSecondFactorValue(FactorValue secondFactorValue)
void	setTstat(Double tstat)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

ContrastResult

public ContrastResult()

Method Detail

getCoefficient

@Nullable
public Double getCoefficient()

Returns:

The estimated value from the fit

setCoefficient

public void setCoefficient(@Nullable
                           Double coefficient)

getFactorValue

@Nullable
public FactorValue getFactorValue()

Returns:

The factorValue for the group of samples that is being compared to baseline. The baseline itself is a property of the ResultSet. For factors that have continuous values, this will be null.

setFactorValue

public void setFactorValue(@Nullable
                           FactorValue factorValue)

getId

public Long getId()

Specified by:

getId in interface Identifiable

setId

public void setId(Long id)

getLogFoldChange

@Nullable
public Double getLogFoldChange()

Returns:

The fold change relative to the baseline, based on the fitted values. log2-transformed. This will be the same as the coefficient if the data were log transformed when analyzed. This might be null if it wasn't computed.

setLogFoldChange

public void setLogFoldChange(@Nullable
                             Double logFoldChange)

getPvalue

@Nullable
public Double getPvalue()

setPvalue

public void setPvalue(@Nullable
                      Double pvalue)

getSecondFactorValue

@Nullable
public FactorValue getSecondFactorValue()

setSecondFactorValue

public void setSecondFactorValue(@Nullable
                                 FactorValue secondFactorValue)

getTstat

@Nullable
public Double getTstat()

Returns:

Serves as the effect size as well as an indicator of the direction of change relative to the baseline

setTstat

public void setTstat(@Nullable
                     Double tstat)

hashCode

public int hashCode()

Overrides:

hashCode in class Object

Returns:

a hash code based on this entity's identifiers.

equals

public boolean equals(Object object)

Overrides:

equals in class Object

Returns:

true if the argument is an ContrastResult instance and all identifiers for this entity equal the identifiers of the argument entity. Returns false otherwise.

toString

public String toString()

Overrides:

toString in class Object