eqtlmappingpipeline.ase.AseVariant Maven / Gradle / Ivy

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package eqtlmappingpipeline.ase;

import cern.colt.list.tdouble.DoubleArrayList;
import cern.colt.list.tint.IntArrayList;
import java.util.ArrayList;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.variant.id.GeneticVariantId;

/**
 *
 * @author Patrick Deelen
 */
public interface AseVariant extends Comparable {

	Allele getA1();

	IntArrayList getA1Counts();

	Allele getA2();

	IntArrayList getA2Counts();

	String getChr();

	double getCountPearsonR();

	GeneticVariantId getId();

	double getMetaPvalue();

	double getMetaZscore();

	AseMleBeta getMle();

	DoubleArrayList getPValues();

	int getPos();

	int getSampleCount();

	ArrayList getSampleIds();

	/**
	 * Can do noting if not applicable
	 */
	void calculateStatistics();

	public double getLikelihoodRatioP();

	public double getLikelihoodRatioD();

	public double getEffect();
}