Package org.snpeff.probablility
Class RankSumNoReplacementSimulate
java.lang.Object
org.snpeff.probablility.RankSumNoReplacementSimulate
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
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionint
getN()
int
long[][]
int[][]
void
Initialize samples (ranks: 1 to N)static void
double
mean
(int nt) void
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) toString()
double
variance
(int nt)
-
Constructor Details
-
RankSumNoReplacementSimulate
public RankSumNoReplacementSimulate(int numberOfSamples, int n)
-
-
Method Details
-
main
-
getN
public int getN() -
getNumberOfSamples
public int getNumberOfSamples() -
getRankSum
public long[][] getRankSum() -
getSamples
public int[][] getSamples() -
initSamples
public void initSamples()Initialize samples (ranks: 1 to N) -
mean
public double mean(int nt) -
randomizeSamples
public void randomizeSamples()Shufle samples (random ranks) -
rankSum
public void rankSum()Calculate rankSums -
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
-
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
-
setN
public void setN(int n) -
setNumberOfSamples
public void setNumberOfSamples(int numberOfSamples) -
setRankSum
public void setRankSum(long[][] rankSum) -
setSamples
public void setSamples(int[][] samples) -
toString
-
variance
public double variance(int nt)
-