Package org.snpeff.probablility
Class RankSumNoReplacementSimulate
- java.lang.Object
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- org.snpeff.probablility.RankSumNoReplacementSimulate
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public class RankSumNoReplacementSimulate extends java.lang.Object
Calculate rank sum probability distribution function (pdf) and cumulative distribution function (cdf). Note: This class assumes that ranks cannot be repeated (selecting without replacement)- Author:
- Pablo Cingolani
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Constructor Summary
Constructors Constructor Description RankSumNoReplacementSimulate(int numberOfSamples, int n)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getN()
int
getNumberOfSamples()
long[][]
getRankSum()
int[][]
getSamples()
void
initSamples()
Initialize samples (ranks: 1 to N)static void
main(java.lang.String[] args)
double
mean(int nt)
void
randomizeSamples()
Shufle samples (random ranks)void
rankSum()
Calculate rankSumsdouble
sampleMean(int nt)
Calculate the mean rankSum for a given 'N_T' (number of ranks to add)double
sampleVariance(int nt)
Calculate the variance of rankSum for a given 'N_T' (number of ranks to add)void
setN(int n)
void
setNumberOfSamples(int numberOfSamples)
void
setRankSum(long[][] rankSum)
void
setSamples(int[][] samples)
java.lang.String
toString()
double
variance(int nt)
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Method Detail
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main
public static void main(java.lang.String[] args)
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getN
public int getN()
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getNumberOfSamples
public int getNumberOfSamples()
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getRankSum
public long[][] getRankSum()
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getSamples
public int[][] getSamples()
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initSamples
public void initSamples()
Initialize samples (ranks: 1 to N)
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mean
public double mean(int nt)
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randomizeSamples
public void randomizeSamples()
Shufle samples (random ranks)
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rankSum
public void rankSum()
Calculate rankSums
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sampleMean
public double sampleMean(int nt)
Calculate the mean rankSum for a given 'N_T' (number of ranks to add)- Parameters:
nt
- : number of ranks to add- Returns:
- Mean rank sum value
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sampleVariance
public double sampleVariance(int nt)
Calculate the variance of rankSum for a given 'N_T' (number of ranks to add)- Parameters:
nt
- : number of ranks to add- Returns:
- Variance rank sum value
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setN
public void setN(int n)
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setNumberOfSamples
public void setNumberOfSamples(int numberOfSamples)
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setRankSum
public void setRankSum(long[][] rankSum)
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setSamples
public void setSamples(int[][] samples)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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variance
public double variance(int nt)
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