ubic.erminej.data

Class GeneSetResult

java.lang.Object

ubic.erminej.data.GeneSetResult

All Implemented Interfaces:

Comparable<GeneSetResult>

Direct Known Subclasses:

EmptyGeneSetResult

public class GeneSetResult
extends Object
implements Comparable<GeneSetResult>

Data structure to store class scoring information about a class. This also knows how to print itself out.

Version:

$Id: GeneSetResult.java,v 1.21 2013/05/20 00:31:10 paul Exp $

Author:

Paul Pavlidis

Field Summary

Fields

Modifier and Type	Field and Description
protected GeneSetTerm	geneSetTerm

Constructor Summary

Constructors

Constructor and Description
GeneSetResult()
GeneSetResult(GeneSetTerm id, int numProbes, int numGenes, double score, double pvalue, double correctedPvalue, SettingsHolder settings)
GeneSetResult(GeneSetTerm id, int numProbes, int numGenes, SettingsHolder settings)

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(GeneSetResult other) Default comparator for this class: sorts by the pvalue.
boolean	equals(Object obj)
double	getCorrectedPvalue()
GeneSetTerm	getGeneSetId()
double	getMfCorrectedFdr()
double	getMfCorrectedPvalue()
Integer	getMultifunctionalityCorrectedRankDelta()
Double	getMultifunctionalityRank()
int	getNumGenes()
int	getNumProbes()
double	getPvalue()
int	getRank() Low numbers are better ranks.
double	getRelativeRank()
double	getScore()
SettingsHolder	getSettings()
int	hashCode()
void	print(Writer out)
void	print(Writer out, String extracolumns) The format is:
void	printHeadings(Writer out)
void	printHeadings(Writer out, String extracolumns)
void	setCorrectedPvalue(double a)
void	setMfCorrectedFdr(double mfCorrectedFdr)
void	setMfCorrectedPvalue(double mfCorrectedPvalue)
void	setMultifunctionalityCorrectedRankDelta(Integer multifunctionalityCorrectedRankDelta) Set how much this result changes in rank when multifunctionality correction is applied.
void	setMultifunctionalityRank(Double rank)
void	setPValue(double apvalue)
void	setRank(int n) Where 1 is the best.
void	setRelativeRank(double i) Where 0 is the best and 1 is the worst.
void	setScore(double ascore)
void	setSizes(int size, int effsize)

Methods inherited from class java.lang.Object

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

Field Detail

geneSetTerm

protected GeneSetTerm geneSetTerm

Constructor Detail

GeneSetResult

public GeneSetResult()

GeneSetResult

public GeneSetResult(GeneSetTerm id,
             int numProbes,
             int numGenes,
             double score,
             double pvalue,
             double correctedPvalue,
             SettingsHolder settings)

Parameters:

id -

name -

numProbes -

numGenes -

score -

pvalue -

GeneSetResult

public GeneSetResult(GeneSetTerm id,
             int numProbes,
             int numGenes,
             SettingsHolder settings)

Parameters:

id -

numProbes - (in set)

numGenes - (in set)

Method Detail

compareTo

public int compareTo(GeneSetResult other)

Default comparator for this class: sorts by the pvalue.

Specified by:

compareTo in interface Comparable<GeneSetResult>

Parameters:

ob - Object

Returns:

int

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

getCorrectedPvalue

public double getCorrectedPvalue()

getGeneSetId

public GeneSetTerm getGeneSetId()

getMfCorrectedFdr

public double getMfCorrectedFdr()

getMfCorrectedPvalue

public double getMfCorrectedPvalue()

getMultifunctionalityCorrectedRankDelta

public Integer getMultifunctionalityCorrectedRankDelta()

getMultifunctionalityRank

public Double getMultifunctionalityRank()

getNumGenes

public int getNumGenes()

Returns:

getNumProbes

public int getNumProbes()

Returns:

int

getPvalue

public double getPvalue()

getRank

public int getRank()

Low numbers are better ranks.

Returns:

getRelativeRank

public double getRelativeRank()

getScore

public double getScore()

getSettings

public SettingsHolder getSettings()

hashCode

public int hashCode()

Overrides:

hashCode in class Object

print

public void print(Writer out)
           throws IOException

Throws:

IOException

print

public void print(Writer out,
         String extracolumns)
           throws IOException

The format is:

 Gene set name
 Gene set ID (e.g. GO:xxxxx)
 Number of probes
 Number of genes
 Score
 Pvalue
 Multiple-testing corrected pvalue (FDR)
 Multifunctionality-corrected pvalue  
 Multifunctionality-corrected pvalue, multiple-test corrected (FDR)  
 Multifunctionality of the gene set (relative rank, 1 is most multifunctional)
 -- One more extra columns such as the redundant gene sets and the gene symbols of the members.
 

Parameters:

out -

extracolumns -

Throws:

IOException

printHeadings

public void printHeadings(Writer out)
                   throws IOException

Throws:

IOException

printHeadings

public void printHeadings(Writer out,
                 String extracolumns)
                   throws IOException

Parameters:

out -

extracolumns -

Throws:

IOException

setCorrectedPvalue

public void setCorrectedPvalue(double a)

setMfCorrectedFdr

public void setMfCorrectedFdr(double mfCorrectedFdr)

setMfCorrectedPvalue

public void setMfCorrectedPvalue(double mfCorrectedPvalue)

setMultifunctionalityCorrectedRankDelta

public void setMultifunctionalityCorrectedRankDelta(Integer multifunctionalityCorrectedRankDelta)

Set how much this result changes in rank when multifunctionality correction is applied. Positive values mean a lot of change.

Parameters:

multifunctionalityCorrectedRankDelta -

setMultifunctionalityRank

public void setMultifunctionalityRank(Double rank)

Parameters:

rank - relative, where 1 is most multifunctional

setPValue

public void setPValue(double apvalue)

setRank

public void setRank(int n)

Where 1 is the best.

Parameters:

n -

setRelativeRank

public void setRelativeRank(double i)

Where 0 is the best and 1 is the worst.

Parameters:

i -

setScore

public void setScore(double ascore)

setSizes

public void setSizes(int size,
            int effsize)