Package org.snpeff.geneSets.algorithm

Class EnrichmentAlgorithmGreedy

java.lang.Object

org.snpeff.geneSets.algorithm.EnrichmentAlgorithm

org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy

Direct Known Subclasses:

EnrichmentAlgorithmGreedyVariableSize

public abstract class EnrichmentAlgorithmGreedy
extends EnrichmentAlgorithm

A generic greedy enrichment algorithm for selecting gene-sets

Author:

pcingola

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm

EnrichmentAlgorithm.EnrichmentAlgorithmType

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	adjustedPvalue
static double	DEFAULT_MAX_PVALUE
protected double	maxPvalue
protected double	maxPvalueAjusted

Fields inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm

HTML_BG_COLOR, HTML_BG_COLOR_TITLE, HTML_TD_GENES_MAX_LEN, PRINT_SOMETHING_TIME

Constructor Summary

Constructors

Constructor	Description
EnrichmentAlgorithmGreedy(GeneSets geneSets, int numberToSelect)

Method Summary

Modifier and Type	Method	Description
protected Result	greedyPvalue(Result prevResult)	Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum)
protected Result	greedyPvalue(Result prevResult, int minGeneSetSize, int maxGeneSetSize)	Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum) Only look for genesets within [minGeneSetSize, maxGeneSetSize] size range
Result	select()	Select the 'best' gene sets
void	setAdjustedPvalue(boolean adjustedPvalue)
void	setMaxGeneSetSize(int maxGeneSetSize)
void	setMaxPvalue(double maxPvalue)
void	setMaxPvalueAjusted(double maxPvalueAjusted)
void	setMinGeneSetSize(int minGeneSetSize)
void	setVerbose(boolean verbose)
protected boolean	stopCriteria(Result result)	Stop criteria

Methods inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm

getMaxPvalueAdjusted, getOutput, isShow, print, setDebug, setFilterOutputGeneSets, setHtmlTable, setMaxPValue, setMaxPvalueAdjusted

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_MAX_PVALUE

public static final double DEFAULT_MAX_PVALUE

See Also:

Constant Field Values

adjustedPvalue

protected boolean adjustedPvalue

maxPvalue

protected double maxPvalue

maxPvalueAjusted

protected double maxPvalueAjusted

Constructor Detail

EnrichmentAlgorithmGreedy

public EnrichmentAlgorithmGreedy(GeneSets geneSets,
                                 int numberToSelect)

Method Detail

greedyPvalue

protected Result greedyPvalue(Result prevResult)

Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum)

Returns:

greedyPvalue

protected Result greedyPvalue(Result prevResult,
                              int minGeneSetSize,
                              int maxGeneSetSize)

Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum) Only look for genesets within [minGeneSetSize, maxGeneSetSize] size range

Returns:

select

public Result select()

Select the 'best' gene sets

Overrides:

select in class EnrichmentAlgorithm

Returns:

setAdjustedPvalue

public void setAdjustedPvalue(boolean adjustedPvalue)

setMaxGeneSetSize

public void setMaxGeneSetSize(int maxGeneSetSize)

Overrides:

setMaxGeneSetSize in class EnrichmentAlgorithm

setMaxPvalue

public void setMaxPvalue(double maxPvalue)

setMaxPvalueAjusted

public void setMaxPvalueAjusted(double maxPvalueAjusted)

setMinGeneSetSize

public void setMinGeneSetSize(int minGeneSetSize)

Overrides:

setMinGeneSetSize in class EnrichmentAlgorithm

setVerbose

public void setVerbose(boolean verbose)

Overrides:

setVerbose in class EnrichmentAlgorithm

stopCriteria

protected boolean stopCriteria(Result result)

Stop criteria

Parameters:

result -

Returns:

true if stop criteria has been met and algorithm should stop iterating.