net.maizegenetics.analysis.gbs

Class Clusters

net.maizegenetics.analysis.gbs.Clusters

public class Clusters

Constructor Detail

Clusters

public Clusters(ReadsByTaxa rbt)

Clusters

public Clusters(TagsByTaxa tbt)

Clusters

public Clusters(java.lang.String infileS,
                boolean binary)

Method Detail

getClusters

public void getClusters(ReadsByTaxa rbt)

getClusters

public void getClusters(TagsByTaxa tbt)

networkFilter

public void networkFilter()

repeatLibraryFilter

public void repeatLibraryFilter(ReadsByTaxa rbt,
                                java.lang.String TagSeqS,
                                java.lang.String repeatlibS)

repeatFilter

public void repeatFilter(ReadsByTaxa rbt,
                         double ratio)

getSnpCount

public int getSnpCount()

alleleFrequencyFileter

public void alleleFrequencyFileter(ReadsByTaxa rbt,
                                   double minBorderMaf,
                                   double maxBorderMaf)

heteozygoteFilter

public void heteozygoteFilter(ReadsByTaxa rbt)

chiSquareDf1

public boolean chiSquareDf1(int ob1,
                            int ob2,
                            int ex1,
                            int ex2,
                            double chiValueCutoff)

chiSquareEvenDf1

public boolean chiSquareEvenDf1(int ob1,
                                int ob2,
                                double chiValueCutoff)

readCluster

public void readCluster(java.lang.String infileS,
                        boolean binary)

hapDetail

public void hapDetail(ReadsByTaxa rbt,
                      java.lang.String outfileS,
                      float coverRate)

writeHapMap

public void writeHapMap(ReadsByTaxa rbt,
                        java.lang.String outfileS,
                        float coverRate)

writeCluster

public void writeCluster(java.lang.String outfileS,
                         boolean binary)

writeFastA

public void writeFastA(ReadsByTaxa rbt,
                       java.lang.String outFastAS)

prin

public void prin()