Class IndependentReplicateMetric


  • @DocumentedFeature(groupName="Metrics",
                       summary="Metrics")
    public class IndependentReplicateMetric
    extends MergeableMetricBase
    A class to store information relevant for biological rate estimation
    • Field Detail

      • nSites

        public Integer nSites
        The count of sites used.
      • nThreeAllelesSites

        public Integer nThreeAllelesSites
        The count of sites in which a third allele was found.
      • nTotalReads

        public Integer nTotalReads
        The total number of reads over the het sites.
      • nDuplicateSets

        public Integer nDuplicateSets
        The number of duplicate sets examined.
      • nExactlyTriple

        public Integer nExactlyTriple
        The number of sets of size exactly 3 found.
      • nExactlyDouble

        public Integer nExactlyDouble
        The number of sets of size exactly 2 found.
      • nReadsInBigSets

        public Integer nReadsInBigSets
        The number of reads in duplicate of sizes greater than 3.
      • nDifferentAllelesBiDups

        public Integer nDifferentAllelesBiDups
        The number of doubletons where the two reads had different bases in the locus.
      • nReferenceAllelesBiDups

        public Integer nReferenceAllelesBiDups
        The number of doubletons where the two reads matched the reference.
      • nAlternateAllelesBiDups

        public Integer nAlternateAllelesBiDups
        The number of doubletons where the two reads matched the alternate.
      • nDifferentAllelesTriDups

        public Integer nDifferentAllelesTriDups
        The number of tripletons where at least one of the reads didn't match either allele of the het site.
      • nMismatchingAllelesBiDups

        public Integer nMismatchingAllelesBiDups
        The number of tripletons where the two reads had different bases in the locus.
      • nReferenceAllelesTriDups

        public Integer nReferenceAllelesTriDups
        The number of tripletons where the two reads matched the reference.
      • nAlternateAllelesTriDups

        public Integer nAlternateAllelesTriDups
        The number of tripletons where the two reads matched the alternate.
      • nMismatchingAllelesTriDups

        public Integer nMismatchingAllelesTriDups
        The number of tripletons where at least one of the reads didn't match either allele of the het site.
      • nReferenceReads

        public Integer nReferenceReads
        The number of reference alleles in the reads.
      • nAlternateReads

        public Integer nAlternateReads
        The number of alternate alleles in the reads.
      • nMismatchingUMIsInDiffBiDups

        public Integer nMismatchingUMIsInDiffBiDups
        The number of UMIs that are different within Bi-sets that come from different alleles.
      • nMatchingUMIsInDiffBiDups

        public Integer nMatchingUMIsInDiffBiDups
        The number of UMIs that are match within Bi-sets that come from different alleles.
      • nMismatchingUMIsInSameBiDups

        public Integer nMismatchingUMIsInSameBiDups
        The number of UMIs that are different within Bi-sets that come from the same alleles.
      • nMatchingUMIsInSameBiDups

        public Integer nMatchingUMIsInSameBiDups
        The number of UMIs that are match within Bi-sets that come from the same alleles.
      • nMismatchingUMIsInCoOrientedBiDups

        public Integer nMismatchingUMIsInCoOrientedBiDups
        The number of bi-sets with mismatching UMIs and same orientation.
      • nMismatchingUMIsInContraOrientedBiDups

        public Integer nMismatchingUMIsInContraOrientedBiDups
        The number of bi-sets with mismatching UMIs and opposite orientation.
      • nBadBarcodes

        public Integer nBadBarcodes
        The number of sets where the UMIs had poor quality bases and were not used for any comparisons.
      • nGoodBarcodes

        public Integer nGoodBarcodes
        the number of sets where the UMIs had good quality bases and were used for any comparisons.
      • biSiteHeterogeneityRate

        public Double biSiteHeterogeneityRate
        the rate of heterogeneity within doubleton sets.
      • triSiteHeterogeneityRate

        public Double triSiteHeterogeneityRate
        the rate of heterogeneity within tripleton sets
      • biSiteHomogeneityRate

        public Double biSiteHomogeneityRate
        the rate of homogeneity within doubleton sets.
      • triSiteHomogeneityRate

        public Double triSiteHomogeneityRate
        the rate of homogeneity within tripleton sets.
      • independentReplicationRateFromBiDups

        public Double independentReplicationRateFromBiDups
      • independentReplicationRateFromTriDups

        public Double independentReplicationRateFromTriDups
        The biological duplication rate (as a fraction of the duplicates sets) calculated from tripleton sets.
      • pSameUmiInIndependentBiDup

        public Double pSameUmiInIndependentBiDup
        When the alleles are different, we know that this is a biological duplication, thus we expect nearly all the UMIs to be different (allowing for equality due to chance). So we expect this to be near 1.
      • pSameAlleleWhenMismatchingUmi

        public Double pSameAlleleWhenMismatchingUmi
        When the UMIs mismatch, we expect about the same number of different alleles as the same (assuming that different UMI implies biological duplicate) thus, this value should be near 0.5
      • independentReplicationRateFromUmi

        public Double independentReplicationRateFromUmi
        Given the UMIs one can estimate the rate of biological duplication directly, as this would be the rate of having different UMIs in all duplicate sets. This is only a good estimate if the assumptions hold, for example if pSameUmiInIndependentBiDup is near 1.
      • replicationRateFromReplicateSets

        public Double replicationRateFromReplicateSets
        An estimate of the duplication rate that is based on the duplicate sets we observed.
    • Constructor Detail

      • IndependentReplicateMetric

        public IndependentReplicateMetric()
    • Method Detail

      • calculateDerivedFields

        public void calculateDerivedFields()
        Description copied from class: MergeableMetricBase
        Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.
        Overrides:
        calculateDerivedFields in class MergeableMetricBase