Examples with Sample function.genotype.base.Sample used on opensource projects

Example 26 with Sample

use of function.genotype.base.Sample in project atav by igm-team.

the class Family method addParentByName.

private void addParentByName(String name) {
    int id = SampleManager.getIdByName(name);
    if (id != Data.NA) {
        Sample parent = SampleManager.getMap().get(id);
        parentList.add(parent);
    }
}

Example 27 with Sample

use of function.genotype.base.Sample in project atav by igm-team.

the class ListVarGeno method processVariant.

@Override
public void processVariant(CalledVariant calledVar) {
    try {
        VarGenoOutput output = new VarGenoOutput(calledVar);
        output.countSampleGeno();
        output.calculate();
        if (output.isValid()) {
            for (Sample sample : SampleManager.getList()) {
                if (isCaseOnlyValid(sample)) {
                    int geno = output.getCalledVariant().getGenotype(sample.getIndex());
                    if (output.isQualifiedGeno(geno)) {
                        bwGenotypes.write(output.getString(sample));
                        bwGenotypes.newLine();
                        SampleVariantCount.update(output.getCalledVariant().isSnv(), geno, sample.getIndex());
                    }
                }
            }
        }
    } catch (Exception e) {
        ErrorManager.send(e);
    }
}

Example 28 with Sample

use of function.genotype.base.Sample in project atav by igm-team.

the class Output method countSampleGeno.

public void countSampleGeno() {
    int geno;
    for (Sample sample : SampleManager.getList()) {
        geno = calledVar.getGenotype(sample.getIndex());
        geno = getGenoType(geno, sample);
        addSampleGeno(geno, sample.getPheno());
    }
}

Example 29 with Sample

use of function.genotype.base.Sample in project atav by igm-team.

the class LogisticRegression method initResponseAndCoviates.

private void initResponseAndCoviates() {
    try {
        // Initializing Params
        // all sample phenotypes
        List<Double> response = new ArrayList<>();
        // all sample covariates per column per list
        List<List<Double>> covariates = new ArrayList<>();
        for (int i = 0; i < SampleManager.getCovariateNum(); i++) {
            covariates.add(new ArrayList<>());
        }
        // Get Data for response and covariates
        for (Sample sample : SampleManager.getList()) {
            response.add((double) sample.getPheno());
            // Set other predictors
            for (int i = 0; i < SampleManager.getCovariateNum(); i++) {
                covariates.get(i).add(sample.getCovariateList().get(i));
            }
        }
        // Set covariate data in Renjin
        String regParam;
        for (int i = 1; i <= SampleManager.getCovariateNum(); i++) {
            regParam = "x" + i;
            MathManager.getRenjinEngine().put(regParam, covariates.get(i - 1));
            MathManager.getRenjinEngine().eval(regParam + " <- as.numeric(unlist(" + regParam + "))");
        }
        // Set response data in Renjin
        MathManager.getRenjinEngine().put("y", response);
        MathManager.getRenjinEngine().eval(" y <- as.numeric(unlist(y))");
        // Initialize expression for covariates plus genotype
        LogisticOutput.initExpression();
    } catch (Exception e) {
        ErrorManager.send(e);
    }
}