Package org.intermine.web.logic.widget

Class EnrichmentCalculation

  • public final class EnrichmentCalculation
extends java.lang.Object
    Calculate enrichment of an attribute applied to members of a sample that is a subset of a larger population. The result is a p-value per attribute that represents the probability that the number of occurrences of the attribute in the sample happened by chance based on the number of occurrences in the population as a whole. Thus a low p-value indicates that the attribute may be characteristic of the items in the sample. Enrichment is implemented using a Hypergeometric test.
    Author:
    Julie Sullivan, Richard Smith, Daniela Butano

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static EnrichmentResults calculate​(EnrichmentInput input, java.lang.Double maxValue, java.lang.String errorCorrection, boolean extraCorrectionCoefficient, CorrectionCoefficient correctionCoefficient)
      Perform an enrichment calculation based on input from some source and return results that include a p-value and count for each attribute that was observed in the sample.

      • Methods inherited from class java.lang.Object

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

    • Method Detail

      • calculate

        public static EnrichmentResults calculate​(EnrichmentInput input,
                                          java.lang.Double maxValue,
                                          java.lang.String errorCorrection,
                                          boolean extraCorrectionCoefficient,
                                          CorrectionCoefficient correctionCoefficient)
        Perform an enrichment calculation based on input from some source and return results that include a p-value and count for each attribute that was observed in the sample. Also perform the type multiple hypothesis error correction specified before returning the results.
        Parameters:
        input - details of the sample and population
        maxValue - the maximum p-value to return, for display purposes
        errorCorrection - the type of error correction to perform or None
        extraCorrectionCoefficient - if true correction coefficient has been selected
        correctionCoefficient - a instance of correction coefficient
        Returns:
        results of the enrichment calculation