net.maizegenetics.analysis.distance

Class GCTADistanceMatrix

net.maizegenetics.analysis.distance.GCTADistanceMatrix

public class GCTADistanceMatrix

Method Detail

getInstance

public static DistanceMatrix getInstance(GenotypeTable genotype)

Compute Normalized_IBS (GCTA) kinship for all pairs of taxa. Missing sites are ignored. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014363/pdf/main.pdf Equation-3

Parameters:

genotype - Genotype Table used to compute kinship

Returns:

org.jetbrains.dokka.NodeRenderContent@8c30591: GCTA Kinship Matrix

getInstance

public static DistanceMatrix getInstance(GenotypeTable genotype,
                                         ProgressListener listener)

Same as other getInstance() but reports progress.

Parameters:

genotype - Genotype Table used to compute kinship

listener - Progress listener

Returns:

org.jetbrains.dokka.NodeRenderContent@23e2b72c: GCTA Kinship Matrix

subtractGCTADistance

public static DistanceMatrix subtractGCTADistance(DistanceMatrixWithCounts[] matrices,
                                                  DistanceMatrixWithCounts superMatrix,
                                                  ProgressListener listener)

addGCTADistance

public static DistanceMatrix addGCTADistance(DistanceMatrixWithCounts[] matrices,
                                             ProgressListener listener)

fireProgress

protected static void fireProgress(int percent,
                                   ProgressListener listener)