Package org.intermine.web.logic.widget

Class EnrichmentResults

  • public class EnrichmentResults
extends java.lang.Object
    A container for results from an Enrichment analysis. An object of this class should contain all information required to display the results of one enrichment calculation.
    Author:
    Richard Smith

    • Constructor Summary

      Constructors 
      Modifier Constructor Description
      protected EnrichmentResults​(java.util.Map<java.lang.String,​java.math.BigDecimal> pValues, java.util.Map<java.lang.String,​java.lang.Integer> counts, java.util.Map<java.lang.String,​java.lang.String> labels, int analysedTotal, java.util.Map<java.lang.String,​PopulationInfo> populationAnnotations, int populationTotal)
      Construct with pre-populated maps from enriched attributes to p-values, counts and labels.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int getAnalysedTotal()
      Get the number of items in the sample that had an attribute value.
      java.util.Map<java.lang.String,​java.lang.Integer> getCounts()
      Get the count of each attribute value found in the sample.
      java.util.Map<java.lang.String,​java.lang.String> getLabels()
      Get additional display labels for attribute values in the enrichment analysis, these may be names where the values analysed were identifiers.
      java.util.Map<java.lang.String,​PopulationInfo> getPopulationAnnotations()
      Get the count of of each attribute value in the population, e.g.
      int getPopulationTotal()
      Get the number of items in the database (or background population) that were annotated.
      java.util.Map<java.lang.String,​java.math.BigDecimal> getPValues()
      Get the probability of enrichment for each attribute value found in the sample.

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • EnrichmentResults

        protected EnrichmentResults​(java.util.Map<java.lang.String,​java.math.BigDecimal> pValues,
                            java.util.Map<java.lang.String,​java.lang.Integer> counts,
                            java.util.Map<java.lang.String,​java.lang.String> labels,
                            int analysedTotal,
                            java.util.Map<java.lang.String,​PopulationInfo> populationAnnotations,
                            int populationTotal)
        Construct with pre-populated maps from enriched attributes to p-values, counts and labels.
        Parameters:
        pValues - calculated p-values per attribute value for this enrichment
        counts - number of items in sample per attribute value
        labels - an additional label for each attribute value, used for display
        analysedTotal - the number of items in the sample that had data for the given attribute
        populationAnnotations - per GO term, number of genes total in database / background population annotated
        populationTotal - total size of the population, e.g. count of genes in the database (or background population)

    • Method Detail

      • getPValues

        public java.util.Map<java.lang.String,​java.math.BigDecimal> getPValues()
        Get the probability of enrichment for each attribute value found in the sample. These may have already undergone error correction.
        Returns:
        a map from attribute value to p-value

      • getCounts

        public java.util.Map<java.lang.String,​java.lang.Integer> getCounts()
        Get the count of each attribute value found in the sample.
        Returns:
        counts of attribute values in the sample.

      • getLabels

        public java.util.Map<java.lang.String,​java.lang.String> getLabels()
        Get additional display labels for attribute values in the enrichment analysis, these may be names where the values analysed were identifiers.
        Returns:
        labels for each attribute value in the sample

      • getPopulationAnnotations

        public java.util.Map<java.lang.String,​PopulationInfo> getPopulationAnnotations()
        Get the count of of each attribute value in the population, e.g. number of total genes annotated per GO term.
        Returns:
        labels for each attribute value in the sample

      • getAnalysedTotal

        public int getAnalysedTotal()
        Get the number of items in the sample that had an attribute value. For example if performing an enrichment on departments present in companies this would return the number of companies in the sample that had any departments at all.
        Returns:
        the number of items in the sample with attribute values

      • getPopulationTotal

        public int getPopulationTotal()
        Get the number of items in the database (or background population) that were annotated. NOTE: This is NOT the count of items in the database. We only include genes that have ANY GO terms because we have a lot of garbage genes.
        Returns:
        the number of items in the population that were annotated with ANY value