org.snpeff.geneSets.algorithm.RankSumPValueGreedyAlgorithm Maven / Gradle / Ivy

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Variant annotation and effect prediction package.

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package org.snpeff.geneSets.algorithm;

import org.apfloat.Apfloat;
import org.snpeff.geneSets.GeneSet;
import org.snpeff.geneSets.GeneSetsRanked;
import org.snpeff.geneSets.Result;
import org.snpeff.probablility.RankSumNoReplacementPdf;

public class RankSumPValueGreedyAlgorithm extends EnrichmentAlgorithmGreedyVariableSize {

	public RankSumPValueGreedyAlgorithm(GeneSetsRanked geneSets, int numberToSelect) {
		super(geneSets, numberToSelect);
	}

	/**
	 * Create a new gene set using all gene sets and calculate pValue
	 * @param geneSetList
	 * @return
	 */
	@Override
	Apfloat pValue(GeneSet geneSet) {
		long rankSum = geneSet.rankSum(); // Make sure rankSum is calculated
		Apfloat pValue = RankSumNoReplacementPdf.get().cdf(((GeneSetsRanked) geneSets).getMaxRank(), geneSet.getRankedGenesCount(), rankSum);
		return pValue;
	}

	/**
	 * Stop criteria
	 * @param result
	 * @return
	 */
	@Override
	protected boolean stopCriteria(Result result) {
		boolean stop = super.stopCriteria(result);
		if (stop) return true;

		// No rank sum? => stop
		GeneSet geneSet = result.getLatestGeneSet();
		if (geneSet.rankSum() <= 0) return true;

		return false;
	}
}