net.maizegenetics.analysis.imputation

Class NucleotideImputationUtils

net.maizegenetics.analysis.imputation.NucleotideImputationUtils

public class NucleotideImputationUtils

Method Detail

callParentAllelesByWindow

public static void callParentAllelesByWindow(PopulationData popdata,
                                             double maxMissing,
                                             double minMaf,
                                             int windowSize,
                                             double minR)

callParentAllelesUsingClusters

public static void callParentAllelesUsingClusters(PopulationData popdata,
                                                  double maxMissing,
                                                  double minMaf,
                                                  int windowSize,
                                                  boolean checkSubpops)

callParentAllelesUsingClustersOnly

public static void callParentAllelesUsingClustersOnly(PopulationData popdata,
                                                      double maxMissing,
                                                      double minMaf,
                                                      int windowSize,
                                                      boolean checkSubpops)

compareHaplotypes

public static boolean compareHaplotypes(kotlin.Array[] h0,
                                        kotlin.Array[] h1,
                                        int overlap,
                                        int haplength)

haplotypeOverlapSimilarity

public static double haplotypeOverlapSimilarity(kotlin.Array[] h0,
                                                kotlin.Array[] h1,
                                                int overlap,
                                                int haplength)

createSubPops

public static void createSubPops(PopulationData popdata,
                                 boolean isNAM)

checksubpops

public static void checksubpops(PopulationData popdata,
                                int halfWindowSize)

translateSitesBackToOriginal

public static kotlin.Array[] translateSitesBackToOriginal(kotlin.Array[] sites,
                                                          kotlin.Array[] translation)

extendClusters

public static java.util.ArrayList<net.maizegenetics.analysis.clustering.HaplotypeCluster> extendClusters(GenotypeTable a,
                                                                                                         java.util.ArrayList<net.maizegenetics.analysis.clustering.HaplotypeCluster> clusters,
                                                                                                         kotlin.Array[] sites,
                                                                                                         kotlin.Array[] windowSize,
                                                                                                         boolean forward)

getMajorAlleleFromSnpset

public static java.lang.String getMajorAlleleFromSnpset(com.google.common.collect.Multiset<java.lang.String> snpset,
                                                        double alpha)

getMajorAlleleFromSnpset

public static java.lang.String getMajorAlleleFromSnpset(com.google.common.collect.Multiset<java.lang.String> snpset)

updateAlleleCalls

public static void updateAlleleCalls(HaplotypeCluster cluster,
                                     kotlin.Array[] sites,
                                     kotlin.Array[] alleleCalls)

callParentAllelesByWindowForBackcrosses

public static void callParentAllelesByWindowForBackcrosses(PopulationData popdata,
                                                           double maxMissing,
                                                           double minMaf,
                                                           int windowSize,
                                                           double minR)

callParentAllelesByWindowForMultipleBC

public static void callParentAllelesByWindowForMultipleBC(PopulationData popdata,
                                                          double maxMissing,
                                                          int minMinorAlleleCount,
                                                          int windowSize)

checkAlignmentOrderIgnoringParents

public static void checkAlignmentOrderIgnoringParents(GenotypeTable[] alignments,
                                                      PopulationData family,
                                                      double r)

getWindows

public static kotlin.Array[] getWindows(BitSet ispoly,
                                        int windowSize)

callParentAllelesUsingTaxaGroups

public static void callParentAllelesUsingTaxaGroups(PopulationData family,
                                                    GenotypeTable[] taxaGroups,
                                                    java.util.LinkedList<java.lang.Integer> snpList)

Parameters:

family - a PopulationData object containing information for this family

taxaGroups - an array of two alignments corresponding to two clusters of taxa

snpList - the list of snps to be called

getIdCorrelation

public static double getIdCorrelation(TaxaList[] id)

whichSitesArePolymorphic

public static BitSet whichSitesArePolymorphic(GenotypeTable a,
                                              double maxMissing,
                                              int minMinorAlleleCount)

whichSitesArePolymorphic

public static BitSet whichSitesArePolymorphic(GenotypeTable a,
                                              double maxMissing,
                                              double minMaf)

whichSitesSegregateCorrectly

public static BitSet whichSitesSegregateCorrectly(GenotypeTable a,
                                                  double maxMissing,
                                                  double ratio)

getTaxaGroupAlignments

public static GenotypeTable[] getTaxaGroupAlignments(GenotypeTable a,
                                                     kotlin.Array[] parentIndex,
                                                     java.util.LinkedList<java.lang.Integer> snpIndices)

computeRForAlleles

public static double computeRForAlleles(int site1,
                                        int site2,
                                        GenotypeTable a)

computeRForMissingness

public static double computeRForMissingness(int site1,
                                            int site2,
                                            GenotypeTable a)

areSameTag

public static boolean areSameTag(int site1,
                                 int site2,
                                 GenotypeTable a)

matchCount

public static kotlin.Array[] matchCount(int site1,
                                        int site2,
                                        GenotypeTable a)

computeGenotypeR

public static double computeGenotypeR(int site1,
                                      int site2,
                                      GenotypeTable a)

imputeUsingViterbiFiveState

public static GenotypeTable imputeUsingViterbiFiveState(GenotypeTable a,
                                                        double probHeterozygous,
                                                        java.lang.String familyName)

imputeUsingViterbiFiveState

public static GenotypeTable imputeUsingViterbiFiveState(GenotypeTable a,
                                                        double probHeterozygous,
                                                        java.lang.String familyName,
                                                        boolean useVariableRecombitionRates)

fillGapsInAlignment

public static void fillGapsInAlignment(PopulationData popdata)

fillGapsInImputedAlignment

public static GenotypeTable fillGapsInImputedAlignment(PopulationData popdata)

convertParentCallsToNucleotides

public static GenotypeTable convertParentCallsToNucleotides(PopulationData popdata)

whichSnpsAreFromSameTag

public static OpenBitSet whichSnpsAreFromSameTag(GenotypeTable geno,
                                                 double minRsq)

whichSnpsAreFromSameTag

public static OpenBitSet whichSnpsAreFromSameTag(GenotypeTable geno,
                                                 BitSet polybits)

filterSnpsByTag

public static GenotypeTable filterSnpsByTag(GenotypeTable a,
                                            double minMaf,
                                            double maxMissing,
                                            double maxHet)

ldfilter

public static BitSet ldfilter(GenotypeTable a,
                              int window,
                              double minR,
                              BitSet filterBits)

neighborLD

public static double neighborLD(GenotypeTable a,
                                int snp,
                                int window,
                                BitSet filterBits)

clusterWindow

public static java.util.ArrayList<net.maizegenetics.analysis.clustering.HaplotypeCluster> clusterWindow(GenotypeTable a,
                                                                                                        int start,
                                                                                                        int length,
                                                                                                        int maxdif)

checkParentage

public static void checkParentage(PopulationData popdata)

Checks whether alleleA is parent1 and alleleC is parent2. If not, switches them.

Parameters:

popdata -