Package org.snpeff.gsa
Class ScoreList
- java.lang.Object
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- org.snpeff.gsa.ScoreList
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- Direct Known Subclasses:
PvaluesList
public class ScoreList extends java.lang.Object
A list of scores- Author:
- pcingola
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
ScoreList.ScoreSummary
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Field Summary
Fields Modifier and Type Field Description static double
SIGNIFICANCE_LEVEL_95
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Constructor Summary
Constructors Constructor Description ScoreList()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(double score)
Add a p-value to the listdouble
avg()
Get averagedouble
avgLargestTop(int topN)
Get average pvalue (largest N)double
avgSmallestTop(int topN)
Get average score (smallest N)double
cdf(double p)
Cumulative distribution function of p-values: P[ pValues <= p ] (i.e.double
cdfUpper(double p)
Cumulative distribution function of p-values: P[ pValues > p ] (i.e.static double
chiSquareCDFComplementary(double chiSquare, int nu)
Upper tail 1 - ChiSquareCDF(p)protected double
getDefaultValue()
java.lang.String
getGeneId()
double
getScore(int index)
double
max()
Get minimum pvaluedouble
min()
Get minimum pvaluedouble
pValueBonferroni()
Minimum p-value corrected using Bonferronidouble
pValueFdr(double alpha)
Combine p-values using FDR procedure References: http://en.wikipedia.org/wiki/False_discovery_ratedouble
pValueFisherChi2()
Combine p-values using Fisher's method References: http://en.wikipedia.org/wiki/Fisher's_methoddouble
pValueSimes()
Combine p-values using Simes's procedure References: http://biomet.oxfordjournals.org/content/73/3/751double
pValueZScore()
Combine p-values using Stouffer's Z-score method References: http://en.wikipedia.org/wiki/Fisher's_method (scroll down to Stouffer's method)double
quantile(double quantile)
Get pvalue quantiledouble
score(ScoreList.ScoreSummary pvalueSummary)
Create a single pValue representing the genevoid
setGeneId(java.lang.String geneId)
int
size()
double
sum()
Get sum of scoresjava.lang.String
toString()
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Field Detail
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SIGNIFICANCE_LEVEL_95
public static final double SIGNIFICANCE_LEVEL_95
- See Also:
- Constant Field Values
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Method Detail
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chiSquareCDFComplementary
public static double chiSquareCDFComplementary(double chiSquare, int nu)
Upper tail 1 - ChiSquareCDF(p)- Parameters:
chiSquare
-nu
-- Returns:
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add
public void add(double score)
Add a p-value to the list- Parameters:
score
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avg
public double avg()
Get average- Returns:
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avgLargestTop
public double avgLargestTop(int topN)
Get average pvalue (largest N)- Returns:
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avgSmallestTop
public double avgSmallestTop(int topN)
Get average score (smallest N)- Returns:
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cdf
public double cdf(double p)
Cumulative distribution function of p-values: P[ pValues <= p ] (i.e. lower tail).- Parameters:
p
-- Returns:
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cdfUpper
public double cdfUpper(double p)
Cumulative distribution function of p-values: P[ pValues > p ] (i.e. upper tail).- Parameters:
p
-- Returns:
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getDefaultValue
protected double getDefaultValue()
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getGeneId
public java.lang.String getGeneId()
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getScore
public double getScore(int index)
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max
public double max()
Get minimum pvalue- Returns:
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min
public double min()
Get minimum pvalue- Returns:
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pValueBonferroni
public double pValueBonferroni()
Minimum p-value corrected using Bonferroni- Returns:
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pValueFdr
public double pValueFdr(double alpha)
Combine p-values using FDR procedure References: http://en.wikipedia.org/wiki/False_discovery_rate- Returns:
- A combined p-value
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pValueFisherChi2
public double pValueFisherChi2()
Combine p-values using Fisher's method References: http://en.wikipedia.org/wiki/Fisher's_method- Returns:
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pValueSimes
public double pValueSimes()
Combine p-values using Simes's procedure References: http://biomet.oxfordjournals.org/content/73/3/751- Returns:
- A combined p-value
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pValueZScore
public double pValueZScore()
Combine p-values using Stouffer's Z-score method References: http://en.wikipedia.org/wiki/Fisher's_method (scroll down to Stouffer's method)- Returns:
- A combined p-value
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quantile
public double quantile(double quantile)
Get pvalue quantile- Returns:
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score
public double score(ScoreList.ScoreSummary pvalueSummary)
Create a single pValue representing the gene- Returns:
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setGeneId
public void setGeneId(java.lang.String geneId)
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size
public int size()
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sum
public double sum()
Get sum of scores- Returns:
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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