net.maizegenetics.analysis.association

Class CompressedMLMusingDoubleMatrix

net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix

public class CompressedMLMusingDoubleMatrix

Constructor Detail

CompressedMLMusingDoubleMatrix

public CompressedMLMusingDoubleMatrix(MLMPlugin parentPlugin,
                                      Datum dataset,
                                      DistanceMatrix kinshipMatrix,
                                      boolean useCompression,
                                      boolean useP3D,
                                      double compression)

CompressedMLMusingDoubleMatrix

public CompressedMLMusingDoubleMatrix(WeightedMLMPlugin parentPlugin,
                                      Datum dataset,
                                      DistanceMatrix kinshipMatrix,
                                      Datum weights,
                                      boolean useCompression,
                                      boolean useP3D,
                                      double compression)

Method Detail

useGenotypeCalls

public void useGenotypeCalls(boolean use)

useReferenceProbability

public void useReferenceProbability(boolean use)

useAlleleProbabilities

public void useAlleleProbabilities(boolean use)

solve

public java.util.List<net.maizegenetics.plugindef.Datum> solve()

formatResults

public java.util.List<net.maizegenetics.plugindef.Datum> formatResults()

computeZKZ

public DoubleMatrix[] computeZKZ(DoubleMatrix data,
                                 DoubleMatrix X,
                                 DoubleMatrix Z,
                                 DistanceMatrix kin,
                                 java.lang.String traitname)

Computes ZKZ. If compression is specified then the compressed ZKZ is calculated along with compressed versions of Z and K.

Parameters:

data - the phenotype data. Needed for optimizing compression.

X - the incidence matrix specifying all fixed effects other than markers

Z - the kinship incidence matrix

kin - the genetic similarity matrix

traitname - the name of the phenotype passed in data

Returns:

org.jetbrains.dokka.NodeRenderContent@2272e1b7: an array containing the Z matrix as its first element and the K matrix as its second element. If compression is specified, then both are the compressed versions.

testMarkerUsingEMMA

public boolean testMarkerUsingEMMA(net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix.CompressedMLMResult result,
                                   DoubleMatrix y,
                                   DoubleMatrix X,
                                   DoubleMatrix K,
                                   DoubleMatrix Z,
                                   int nAlleles,
                                   java.util.ArrayList<java.lang.Byte> markerIds)

testMarkerUsingP3D

public void testMarkerUsingP3D(net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix.CompressedMLMResult result,
                               DoubleMatrix y,
                               DoubleMatrix X,
                               DoubleMatrix invV,
                               int markerdf,
                               java.util.ArrayList<java.lang.Byte> markerIds)

calculateV

public DoubleMatrix calculateV(DoubleMatrix ZKZ,
                               double genvar,
                               double resvar)

calculateV

public DoubleMatrix calculateV(DoubleMatrix ZKZ,
                               DoubleMatrix W,
                               double genvar,
                               double resvar)

calculateDistanceFromKin

public DistanceMatrix calculateDistanceFromKin(DistanceMatrix kin)

updateMissingWithKinship

public TaxaList updateMissingWithKinship(BitSet missing,
                                         Taxon[] phenotypeTaxa)

Parameters:

missing - a BitSet with bits equal set when a value is missing in that row

phenotypeTaxa - the taxa

Returns:

org.jetbrains.dokka.NodeRenderContent@34f95205: a TaxaList with the taxa that are in both the kinship matrix and the phenotype. Sets indices of taxa in missing that are not in the kinship matrix.

createResPhenotype

public Datum createResPhenotype(EMMAforDoubleMatrix emma,
                                java.util.List<net.maizegenetics.taxa.Taxon> taxa,
                                java.lang.String traitName)

setTestMarkers

public void setTestMarkers(boolean testMarkers)