Package org.snpeff.probablility

Class RankSumNoReplacementPdf

java.lang.Object
org.snpeff.probablility.RankSumNoReplacementPdf
public class RankSumNoReplacementPdf extends 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

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static int
    CACHE_MAX_N
    Cache size roughly (N * NT)^2
    static String
    DEFAULT_CACHE_FILE
     
    static int
    warnCDF
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    cacheSetPdf(int n, int nt, long r, double pdf)
     
    boolean
    canBeCached(int n, int nt)
    Is the number in the cache
    org.apfloat.Apfloat
    cdf(int n, int nt, long r)
    Probability of getting a rank sum less or equal to 'r' when adding the ranks of 'nt' selected items.
    org.apfloat.Apfloat
    cdfExact(int n, int nt, long r)
    Cumulative density function (cdf)
    org.apfloat.Apfloat
    cdfNormal(int n, int nt, long r)
    Normal approximation to rankSum CDF
    org.apfloat.Apfloat
    cdfTriangle(int n, int nt, long r)
    Uniform 'approximation' to rank sum statistic
    org.apfloat.Apfloat
    cdfUniform(int n, int nt, long r)
    Uniform 'approximation' to rank sum statistic
    void
    createCacheFile()
    Create a cache file
    static RankSumNoReplacementPdf
    get()
     
    String
    getCacheFile()
     
    long
    maxRankSum(int n, int nt)
    Maximum possible rank sum
    double
    mean(int n, int nt)
    Mean value for a given N and N_T
    long
    minRankSum(int n, int nt)
    Minimum possible rank sum
    org.apfloat.Apfloat
    pdf(int n, int nt, long r)
    Probability of getting a rank sum equal to 'r' when adding the ranks of 'nt' selected items.
    org.apfloat.Apfloat
    pdfExact(int n, int nt, long r)
    Probability of getting a rank sum equal to 'r' when adding the ranks of 'nt' selected items.
    org.apfloat.Apfloat
    pdfExact(int n, int nt, long r, long rmin, int out)
    Probability density function (pdf): Exact calculation
    org.apfloat.Apfloat
    pdfNormal(int n, int nt, long r)
    Normal approximation to rank sum statistic
    org.apfloat.Apfloat
    pdfTriangle(int n, int nt, long r)
    Uniform 'approximation' to rank sum statistic
    org.apfloat.Apfloat
    pdfUniform(int n, int nt, long r)
    Uniform 'approximation' to rank sum statistic
    void
    readCacheFile()
    Read cache file
    void
    setCacheFile(String cacheFile)
     
    double
    sigma(int n, int nt)
    Wrapper to Sqrt(variance)
    String
    toStringCache()
    Some cache statistics
    double
    variance(int n, int nt)
    Variance for a given N and N_T
    double
    varianceSlow(int n, int nt)
    Variance for a given N and N_T (slow method, only used for debugging)

    Methods inherited from class java.lang.Object

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

  • Field Details

    • CACHE_MAX_N

      public static int CACHE_MAX_N
      Cache size roughly (N * NT)^2

    • DEFAULT_CACHE_FILE

      public static String DEFAULT_CACHE_FILE

    • warnCDF

      public static int warnCDF

  • Method Details

    • get

      public static RankSumNoReplacementPdf get()

    • cacheSetPdf

      public void cacheSetPdf(int n, int nt, long r, double pdf)

    • canBeCached

      public boolean canBeCached(int n, int nt)
      Is the number in the cache
      Returns:
      true if it is

    • cdf

      public org.apfloat.Apfloat cdf(int n, int nt, long r)
      Probability of getting a rank sum less or equal to 'r' when adding the ranks of 'nt' selected items. Items are ranked '1..n' (from 1 to 'n') Note: Approximated when 'n > 30'
      Parameters:
      n - : Maximum rank number
      nt - : Number of elements in the sum
      r - : rank sum value
      Returns:

    • cdfExact

      public org.apfloat.Apfloat cdfExact(int n, int nt, long r)
      Cumulative density function (cdf)
      Parameters:
      n - : Maximum rank number
      nt - : Number of elements in the sum
      r - : rank sum value
      Returns:
      The probability that selecting 'nt' elements out of 'n' ranked elements, the rank sum is less or equal to 'r'

    • cdfNormal

      public org.apfloat.Apfloat cdfNormal(int n, int nt, long r)
      Normal approximation to rankSum CDF
      Parameters:
      n - : Maximum rank number
      nt - : Number of elements in the sum
      r - : rank sum value
      Returns:
      The probability that selecting 'nt' elements out of 'n' ranked elements, the rank sum is less or equal to 'r'

    • cdfTriangle

      public org.apfloat.Apfloat cdfTriangle(int n, int nt, long r)
      Uniform 'approximation' to rank sum statistic
      Parameters:
      n - : Maximum rank number
      nt - : Number of elements in the sum
      dr - : rank sum value
      Returns:
      The probability that selecting 'nt' elements out of 'n' ranked elements, the rank sum is equal to 'r'

    • cdfUniform

      public org.apfloat.Apfloat cdfUniform(int n, int nt, long r)
      Uniform 'approximation' to rank sum statistic
      Parameters:
      n - : Maximum rank number
      nt - : Number of elements in the sum
      r - : rank sum value
      Returns:
      The probability that selecting 'nt' elements out of 'n' ranked elements, the rank sum is equal to 'r'

    • createCacheFile

      public void createCacheFile()
      Create a cache file
      Parameters:
      fileName -

    • getCacheFile

      public String getCacheFile()

    • maxRankSum

      public long maxRankSum(int n, int nt)
      Maximum possible rank sum
      Parameters:
      n -
      nt -
      Returns:

    • mean

      public double mean(int n, int nt)
      Mean value for a given N and N_T
      Parameters:
      n -
      nt -
      Returns:

    • minRankSum

      public long minRankSum(int n, int nt)
      Minimum possible rank sum
      Parameters:
      n -
      nt -
      Returns:

    • pdf

      public org.apfloat.Apfloat pdf(int n, int nt, long r)
      Probability of getting a rank sum equal to 'r' when adding the ranks of 'nt' selected items. Items are ranked '1..n' (from 1 to 'n') Note: Approximated when 'n > 30'
      Parameters:
      n - : Maximum rank number
      nt - : Number of elements in the sum
      r - : rank sum value
      Returns:

    • pdfExact

      public org.apfloat.Apfloat pdfExact(int n, int nt, long r)
      Probability of getting a rank sum equal to 'r' when adding the ranks of 'nt' selected items. Items are ranked '1..n' (from 1 to 'n') Note: Exact calculation Wrapper to 'real' pdf function
      Parameters:
      n - : Maximum rank number
      nt - : Number of elements in the sum
      r - : rank sum value
      Returns:

    • pdfExact

      public org.apfloat.Apfloat pdfExact(int n, int nt, long r, long rmin, int out)
      Probability density function (pdf): Exact calculation
      Parameters:
      n - : Maximum rank number
      nt - : Number of elements in the sum
      r - : rank sum value
      Returns:
      The probability that selecting 'nt' elements out of 'n' ranked elements, the rank sum is equal to 'r'

    • pdfNormal

      public org.apfloat.Apfloat pdfNormal(int n, int nt, long r)
      Normal approximation to rank sum statistic
      Parameters:
      n - : Maximum rank number
      nt - : Number of elements in the sum
      r - : rank sum value
      Returns:
      The probability that selecting 'nt' elements out of 'n' ranked elements, the rank sum is equal to 'r'

    • pdfTriangle

      public org.apfloat.Apfloat pdfTriangle(int n, int nt, long r)
      Uniform 'approximation' to rank sum statistic
      Parameters:
      n - : Maximum rank number
      nt - : Number of elements in the sum
      dr - : rank sum value
      Returns:
      The probability that selecting 'nt' elements out of 'n' ranked elements, the rank sum is equal to 'r'

    • pdfUniform

      public org.apfloat.Apfloat pdfUniform(int n, int nt, long r)
      Uniform 'approximation' to rank sum statistic
      Parameters:
      n - : Maximum rank number
      nt - : Number of elements in the sum
      r - : rank sum value
      Returns:
      The probability that selecting 'nt' elements out of 'n' ranked elements, the rank sum is equal to 'r'

    • readCacheFile

      public void readCacheFile()
      Read cache file

    • setCacheFile

      public void setCacheFile(String cacheFile)

    • sigma

      public double sigma(int n, int nt)
      Wrapper to Sqrt(variance)
      Parameters:
      n -
      nt -
      Returns:

    • toStringCache

      public String toStringCache()
      Some cache statistics
      Returns:

    • variance

      public double variance(int n, int nt)
      Variance for a given N and N_T
      Parameters:
      n -
      nt -
      Returns:

    • varianceSlow

      public double varianceSlow(int n, int nt)
      Variance for a given N and N_T (slow method, only used for debugging)
      Parameters:
      n -
      nt -
      Returns: