Package org.snpeff.gsa
Class ScoreList
java.lang.Object
org.snpeff.gsa.ScoreList
- Direct Known Subclasses:
PvaluesList
A list of scores
- Author:
- pcingola
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Nested Class Summary
Nested Classes -
Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
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
double
getScore
(int index) double
max()
Get minimum pvaluedouble
min()
Get minimum pvaluedouble
Minimum p-value corrected using Bonferronidouble
pValueFdr
(double alpha) Combine p-values using FDR procedure References: http://en.wikipedia.org/wiki/False_discovery_ratedouble
Combine p-values using Fisher's method References: http://en.wikipedia.org/wiki/Fisher's_methoddouble
Combine p-values using Simes's procedure References: http://biomet.oxfordjournals.org/content/73/3/751double
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
int
size()
double
sum()
Get sum of scorestoString()
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Field Details
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SIGNIFICANCE_LEVEL_95
public static final double SIGNIFICANCE_LEVEL_95- See Also:
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Constructor Details
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ScoreList
public ScoreList()
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Method Details
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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() -
getGeneId
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getScore
public double getScore(int index) -
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
Create a single pValue representing the gene- Returns:
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setGeneId
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size
public int size() -
sum
public double sum()Get sum of scores- Returns:
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toString
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