Examples with AlleleFractionModeller org.broadinstitute.hellbender.tools.exome.allelefraction.AlleleFractionModeller used on opensource projects

Example 1 with AlleleFractionModeller

use of org.broadinstitute.hellbender.tools.exome.allelefraction.AlleleFractionModeller in project gatk-protected by broadinstitute.

the class ACNVModeller method fitModel.

/**
     * Performs Markov-Chain Monte Carlo model fitting using the
     * number of total samples and number of burn-in samples pecified at construction.
     */
public void fitModel() {
    //perform MCMC to generate posterior samples
    logger.info("Fitting copy-ratio model...");
    copyRatioModeller = new CopyRatioModeller(segmentedGenome);
    copyRatioModeller.fitMCMC(numSamplesCopyRatio, numBurnInCopyRatio);
    logger.info("Fitting allele-fraction model...");
    alleleFractionModeller = new AlleleFractionModeller(segmentedGenome, allelicPoN);
    alleleFractionModeller.fitMCMC(numSamplesAlleleFraction, numBurnInAlleleFraction);
    //update list of ACNVModeledSegment with new PosteriorSummaries
    segments.clear();
    final List<SimpleInterval> unmodeledSegments = segmentedGenome.getSegments();
    final List<PosteriorSummary> segmentMeansPosteriorSummaries = copyRatioModeller.getSegmentMeansPosteriorSummaries(CREDIBLE_INTERVAL_ALPHA, ctx);
    final List<PosteriorSummary> minorAlleleFractionsPosteriorSummaries = alleleFractionModeller.getMinorAlleleFractionsPosteriorSummaries(CREDIBLE_INTERVAL_ALPHA, ctx);
    for (int segment = 0; segment < unmodeledSegments.size(); segment++) {
        segments.add(new ACNVModeledSegment(unmodeledSegments.get(segment), segmentMeansPosteriorSummaries.get(segment), minorAlleleFractionsPosteriorSummaries.get(segment)));
    }
    isModelFit = true;
}

Example 2 with AlleleFractionModeller

use of org.broadinstitute.hellbender.tools.exome.allelefraction.AlleleFractionModeller in project gatk by broadinstitute.

the class ACNVModeller method fitModel.

/**
     * Performs Markov-Chain Monte Carlo model fitting using the
     * number of total samples and number of burn-in samples pecified at construction.
     */
public void fitModel() {
    //perform MCMC to generate posterior samples
    logger.info("Fitting copy-ratio model...");
    copyRatioModeller = new CopyRatioModeller(segmentedGenome);
    copyRatioModeller.fitMCMC(numSamplesCopyRatio, numBurnInCopyRatio);
    logger.info("Fitting allele-fraction model...");
    alleleFractionModeller = new AlleleFractionModeller(segmentedGenome, allelicPoN);
    alleleFractionModeller.fitMCMC(numSamplesAlleleFraction, numBurnInAlleleFraction);
    //update list of ACNVModeledSegment with new PosteriorSummaries
    segments.clear();
    final List<SimpleInterval> unmodeledSegments = segmentedGenome.getSegments();
    final List<PosteriorSummary> segmentMeansPosteriorSummaries = copyRatioModeller.getSegmentMeansPosteriorSummaries(CREDIBLE_INTERVAL_ALPHA, ctx);
    final List<PosteriorSummary> minorAlleleFractionsPosteriorSummaries = alleleFractionModeller.getMinorAlleleFractionsPosteriorSummaries(CREDIBLE_INTERVAL_ALPHA, ctx);
    for (int segment = 0; segment < unmodeledSegments.size(); segment++) {
        segments.add(new ACNVModeledSegment(unmodeledSegments.get(segment), segmentMeansPosteriorSummaries.get(segment), minorAlleleFractionsPosteriorSummaries.get(segment)));
    }
    isModelFit = true;
}