Constructor Detail

• ContigencyTable

  public ContigencyTable(int maxSize)

  constructor for Contigency table

  Parameters:

  maxSize - is the maximum sum that will be encountered by contigency table

Method Detail

• setMatrix

  public void setMatrix(int[][] tcontig)

  sets the data for the contigency table, must be set before other methods are called. If tcontig has a greater count than maxSize, then the contig is set to null

  Parameters:

  contig - is the array of integers with observed states

• calcRapidContigencyChiSquare

  public double calcRapidContigencyChiSquare(int maxPermutations)

  This calculates the probability in a rapid approach, using the Chi Square as the test statistic. It runs for maxPermutations permutations unless it find 10 values that beat the observed, and then it stops and calculates the p-value. This slighly biases the P-values but makes it much more rapid.

  Parameters:

  maxPermutations - Number of permutations used to calculate the probability

  Returns:

  P-value (NaN is returned if bad contig was set)

• calcContigencyChiSquare

  public double calcContigencyChiSquare(int permutations)

  This calculates the probability in the normal approach, using the Chi Square as the test statistic.

  Parameters:

  permutations - Number of permutations used to calculate the probability

  Returns:

  P-value (NaN is returned if bad contig was set)

• calcRapidMonteCarloExactTest

  public double calcRapidMonteCarloExactTest(int maxPermutations)

  This calculates the probability in the rapid permutational approach, using the method described by Weir, B. S. (1996) Genetic Data Analysis II (Sinauer, Sunderland, MA) It runs for 1000 permutations unless it find 10 values that beat the observed, and then it stops and calculates the p-value. This slighly biases the P-values but makes it much more rapid.

  Parameters:

  reps - is the number of permutations used to the probability

  Returns:

  P-value (NaN is returned if bad contig was set)

• calcMonteCarloExactTest

  public double calcMonteCarloExactTest(int permutations)

  This calculates the probability in the normal permutation approach, using the method described by Weir, B. S. (1996) Genetic Data Analysis II (Sinauer, Sunderland, MA).

  Parameters:

  permutations - Number of permutations used to the probability

  Returns:

  P-value (NaN is returned if bad contig was set)