net.maizegenetics.analysis.association.AlleleProbabilityFELM Maven / Gradle / Ivy

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TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
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package net.maizegenetics.analysis.association;

import java.util.ArrayList;

import net.maizegenetics.dna.snp.score.AlleleProbability;
import net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE;
import net.maizegenetics.plugindef.Datum;
import net.maizegenetics.stats.linearmodels.CovariateModelEffect;
import net.maizegenetics.stats.linearmodels.LinearModelUtils;
import net.maizegenetics.stats.linearmodels.ModelEffect;
import net.maizegenetics.stats.linearmodels.SweepFastLinearModel;
import net.maizegenetics.util.BitSet;
import net.maizegenetics.util.OpenBitSet;

public class AlleleProbabilityFELM extends AbstractFixedEffectLM {

	public AlleleProbabilityFELM(Datum data, FixedEffectLMPlugin parentPlugin) {
		super(data, parentPlugin);
	}
	
	@Override
	protected void analyzeSite() {
		String siteName = myGenoPheno.genotypeTable().siteName(myCurrentSite);
		SweepFastLinearModel markerModel = null;
		ArrayList modelPlusMarkers = new ArrayList<>(myBaseModel);

		//retrieve values at this site, get A,C,G, and T, gap, insertion values
		//delete any that are monomorphic
		//if remaining sum to a vector of 1's drop one

		//retrieve values for A,C,G,T,gap,insertion and test for monomorphic
		int ntaxa = myGenoPheno.genotypeTable().numberOfTaxa();
		float[] sumOfValues = new float[ntaxa];
		ArrayList probList = new ArrayList<>();
		ArrayList typeList = new ArrayList<>();
		for (SITE_SCORE_TYPE type : AlleleProbability.ALLELE_PROBABILITY_TYPES) {
			float[] values = myGenoPheno.alleleProbsOfType(type, myCurrentSite);
			if (!AssociationUtils.isMonomorphic(values)) {
				probList.add(values);
				typeList.add(type);
				for (int t = 0; t < ntaxa; t++) sumOfValues[t] += values[t];
			}
		}

		//do the arrays sum to an array of ones?
		//since the byte conversion is approximate use 0.95 to 1.05 to test
		boolean sumsToOne = true;
		for (int t = 0; t < ntaxa; t++) {
			if (sumOfValues[t] < 0.95 || sumOfValues[t] > 1.05) {
				sumsToOne = false;
				break;
			}
		}

		//add the alleles as ModelEffects
		int numberOfAlleles = probList.size();
		int numberOfAllelesInModel = numberOfAlleles;
		if (sumsToOne) numberOfAllelesInModel--;
		for (int a = 0; a < numberOfAllelesInModel; a++) {
			double[] covar = AssociationUtils.getNonMissingDoubles(probList.get(a), missingObsForSite);
			modelPlusMarkers.add(new CovariateModelEffect(covar));
		}

		if (areTaxaReplicated) myModel.add(taxaEffect());

		//solve the model
		markerModel = new SweepFastLinearModel(modelPlusMarkers, siteData);

        //calculate model
        double[] modelSSdf = markerModel.getModelcfmSSdf();
        if (areTaxaReplicated) errorSSdf = markerModel.getIncrementalSSdf(taxaEffectNumber);
        else errorSSdf = markerModel.getResidualSSdf();
        markerSSdf = new double[]{0,0};
        for (int a = 0; a < numberOfAllelesInModel; a++) {
        	double[] SSdf = markerModel.getIncrementalSSdf(a + numberOfBaseEffects);
        	markerSSdf[0] += SSdf[0];
        	markerSSdf[1] += SSdf[1];
        }
        double rsq = markerSSdf[0] / (modelSSdf[0] + errorSSdf[0]);
        
        double F = markerSSdf[0] / markerSSdf[1] / errorSSdf[0] * errorSSdf[1];
        double p;
        try {
            p = LinearModelUtils.Ftest(F, markerSSdf[1], errorSSdf[1]);
        } catch (Exception e) {
            p = Double.NaN;
        }
        double[] beta = markerModel.getBeta();
		
        //add results to site report
        //{"Trait","Marker","Chr","Position","marker_F","marker_p","marker_Rsq","marker_df","marker_MS","error_df","error_MS","model_df","model_MS" }
        Object[] rowData = new Object[numberOfSiteReportColumns];
        int columnCount = 0;
        rowData[columnCount++] = currentTraitName;
        rowData[columnCount++] = siteName;	
        rowData[columnCount++] = myGenoPheno.genotypeTable().chromosomeName(myCurrentSite);
        rowData[columnCount++] = myGenoPheno.genotypeTable().chromosomalPosition(myCurrentSite);
        rowData[columnCount++] = new Double(F);
        rowData[columnCount++] = new Double(p);
        rowData[columnCount++] = new Double(rsq);
        rowData[columnCount++] = new Double(markerSSdf[1]);
        rowData[columnCount++] = new Double(markerSSdf[0]/markerSSdf[1]);
        rowData[columnCount++] = new Double(errorSSdf[1]);
        rowData[columnCount++] = new Double(errorSSdf[0]/errorSSdf[1]);
        rowData[columnCount++] = new Double(modelSSdf[1]);
        rowData[columnCount++] = new Double(modelSSdf[0]/modelSSdf[1]);
        siteReportBuilder.add(rowData);
        
        //add results to allele report
        //{"Trait","Marker","Chr","Position","Allele","Estimate"}
        int firstEstimateIndex = beta.length - numberOfAllelesInModel;
        for (int a = 0; a < numberOfAlleles; a++) {
            rowData = new Object[numberOfAlleleReportColumns];
            columnCount = 0;
            rowData[columnCount++] = currentTraitName;
            rowData[columnCount++] = siteName;
            rowData[columnCount++] = myGenoPheno.genotypeTable().chromosomeName(myCurrentSite);
            rowData[columnCount++] = myGenoPheno.genotypeTable().chromosomalPosition(myCurrentSite);
            rowData[columnCount++] = typeNameMap.get(typeList.get(a));
            if (a < numberOfAllelesInModel) rowData[columnCount++] = new Double(beta[firstEstimateIndex + a]);
            else rowData[columnCount++] = new Double(0.0);
            alleleReportBuilder.add(rowData);
        }
     
	}

	@Override
	protected void getGenotypeAndUpdateMissing(BitSet missingObsBeforeSite) {
		float[] allSiteProbs = myGenoPheno.alleleProbsOfType(SITE_SCORE_TYPE.ProbA, myCurrentSite);
		int n = allSiteProbs.length;
		missingObsForSite = new OpenBitSet(missingObsBeforeSite);
		for (int i = 0; i < n; i++) {
			if (Float.isNaN(allSiteProbs[i])) missingObsForSite.fastSet(i);
		}
	}

	@Override
	protected void getGenotypeAfterUpdatingMissing() {
		// TODO Auto-generated method stub
		//does nothing
	}


}