Examples with PurityAdjuster com.hartwig.hmftools.common.purple.PurityAdjuster used on opensource projects

Example 6 with PurityAdjuster

use of com.hartwig.hmftools.common.purple.PurityAdjuster in project hmftools by hartwigmedical.

the class LoadStructuralVariants method enrichStructuralVariants.

@NotNull
private static List<EnrichedStructuralVariant> enrichStructuralVariants(@NotNull List<StructuralVariant> variants, @NotNull DatabaseAccess dbAccess, @NotNull String tumorSample) {
    final PurityContext purityContext = dbAccess.readPurityContext(tumorSample);
    if (purityContext == null) {
        LOGGER.warn("Unable to retrieve purple data. Enrichment may be incomplete.");
    }
    final PurityAdjuster purityAdjuster = purityContext == null ? new PurityAdjuster(Gender.FEMALE, 1, 1) : new PurityAdjuster(purityContext.gender(), purityContext.bestFit().purity(), purityContext.bestFit().normFactor());
    final List<PurpleCopyNumber> copyNumberList = dbAccess.readCopynumbers(tumorSample);
    final Multimap<String, PurpleCopyNumber> copyNumbers = Multimaps.index(copyNumberList, PurpleCopyNumber::chromosome);
    return EnrichedStructuralVariantFactory.enrich(variants, purityAdjuster, copyNumbers);
}

Example 7 with PurityAdjuster

use of com.hartwig.hmftools.common.purple.PurityAdjuster in project hmftools by hartwigmedical.

the class StructuralVariantPloidyFactoryTest method testPurityAdjustedPloidy.

@Test
public void testPurityAdjustedPloidy() {
    final StructuralVariantLeg leg = createLeg(1001, 1, 0.5);
    final List<PurpleCopyNumber> copyNumbers = Lists.newArrayList(copyNumber(1, 1000, 2), copyNumber(1001, 200, 1));
    Optional<ModifiableStructuralVariantLegPloidy> purePloidy = PURE_PLOIDY_FACTORY.create(leg, GenomeRegionSelectorFactory.create(copyNumbers));
    assertPloidy(1d, purePloidy);
    final PurityAdjuster diluted = new PurityAdjuster(Gender.FEMALE, 0.8, 1);
    final StructuralVariantLegPloidyFactory<PurpleCopyNumber> dilutedFactory = new StructuralVariantLegPloidyFactory<>(diluted, PurpleCopyNumber::averageTumorCopyNumber);
    Optional<ModifiableStructuralVariantLegPloidy> dilutedPloidy = dilutedFactory.create(leg, GenomeRegionSelectorFactory.create(copyNumbers));
    assertPloidy(1.25d, dilutedPloidy);
    final PurityAdjuster male = new PurityAdjuster(Gender.MALE, 0.8, 1);
    final StructuralVariantLegPloidyFactory<PurpleCopyNumber> maleFactory = new StructuralVariantLegPloidyFactory<>(male, PurpleCopyNumber::averageTumorCopyNumber);
    Optional<ModifiableStructuralVariantLegPloidy> malePloidy = maleFactory.create(leg, GenomeRegionSelectorFactory.create(copyNumbers));
    assertPloidy(1.125d, malePloidy);
}

Example 8 with PurityAdjuster

use of com.hartwig.hmftools.common.purple.PurityAdjuster in project hmftools by hartwigmedical.

the class ClonalityTest method testClonality.

@Test
public void testClonality() {
    final String chromosome = "1";
    final PurityAdjuster purityAdjuster = new PurityAdjuster(Gender.FEMALE, 0.3, 1);
    assertEquals(Clonality.SUBCLONAL, Clonality.fromSample(purityAdjuster, chromosome, 3, create(4, 100)));
    assertEquals(Clonality.CLONAL, Clonality.fromSample(purityAdjuster, chromosome, 3, create(5, 100)));
    assertEquals(Clonality.CLONAL, Clonality.fromSample(purityAdjuster, chromosome, 3, create(60, 100)));
    assertEquals(Clonality.INCONSISTENT, Clonality.fromSample(purityAdjuster, chromosome, 3, create(61, 100)));
}