net.maizegenetics.analysis.popgen

Class DiversityAnalyses

AbstractTableReport

net.maizegenetics.analysis.popgen.DiversityAnalyses

All Implemented Interfaces:

TableReport

public class DiversityAnalyses
extends AbstractTableReport
implements TableReport

This method calculated estimates of nucleotide diversity (pi, theta, etc). In order to provide high performance, it establishes one nucleotide SitePattern, and then manipulates the weighting patterns for sliding windows and different types of sites. Total segregating sites needs to be adjusted for missing and gap data, as this will modify Theta and Tajima estimates

Constructor Detail

DiversityAnalyses

public DiversityAnalyses(GenotypeTable aa,
                         boolean slidingWindow,
                         int start,
                         int end,
                         int window,
                         int step,
                         PolymorphismDistribution thePolymorphismDistribution)

Constructor that uses a sliding window

Parameters:

aa - an annotated alignment

slidingWindow - if true a sliding window will be run

DiversityAnalyses

public DiversityAnalyses(GenotypeTable aa,
                         boolean slidingWindow,
                         int start,
                         int end,
                         int window,
                         int step)

Method Detail

estimateTheta

public static double estimateTheta(int segSites,
                                   int totalSites,
                                   double averageSiteCoverage,
                                   int taxa)

estimateThetaPerbp

public static double estimateThetaPerbp(int segSites,
                                        int totalSites,
                                        double averageSiteCoverage,
                                        int taxa)

estimatePi

public static double estimatePi(int totalSites,
                                double avgPairwiseDivergence,
                                double averageSiteCoverage)

estimatePiPerbp

public static double estimatePiPerbp(int totalSites,
                                     double avgPairwiseDivergence,
                                     double averageSiteCoverage)

estimateTajimaD

public static double estimateTajimaD(int segSites,
                                     double totalSites,
                                     double averageSiteCoverage,
                                     double taxa,
                                     double pipbp,
                                     double thetapbp)

getTableColumnNames

public java.lang.Object[] getTableColumnNames()

getRow

public java.lang.Object[] getRow(long row)

Returns specified row.

Parameters:

row - row number

Returns:

org.jetbrains.dokka.NodeRenderContent@a8705fe: row

getTableTitle

public java.lang.String getTableTitle()

toString

public java.lang.String toString()

getRowCount

public long getRowCount()

getElementCount

public long getElementCount()

getColumnCount

public int getColumnCount()