Class EnrichmentAlgorithmGreedy

    • Field Detail

      • adjustedPvalue

        protected boolean adjustedPvalue
      • maxPvalue

        protected double maxPvalue
      • maxPvalueAjusted

        protected double maxPvalueAjusted
    • Constructor Detail

      • EnrichmentAlgorithmGreedy

        public EnrichmentAlgorithmGreedy​(GeneSets geneSets,
                                         int numberToSelect)
    • Method Detail

      • greedyPvalue

        protected Result greedyPvalue​(Result prevResult)
        Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum)
        Returns:
      • greedyPvalue

        protected Result greedyPvalue​(Result prevResult,
                                      int minGeneSetSize,
                                      int maxGeneSetSize)
        Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum) Only look for genesets within [minGeneSetSize, maxGeneSetSize] size range
        Returns:
      • setAdjustedPvalue

        public void setAdjustedPvalue​(boolean adjustedPvalue)
      • setMaxPvalue

        public void setMaxPvalue​(double maxPvalue)
      • setMaxPvalueAjusted

        public void setMaxPvalueAjusted​(double maxPvalueAjusted)
      • stopCriteria

        protected boolean stopCriteria​(Result result)
        Stop criteria
        Parameters:
        result -
        Returns:
        true if stop criteria has been met and algorithm should stop iterating.