net.maizegenetics.analysis.gbs.repgen

Class RepGenLDAnalysisPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class RepGenLDAnalysisPlugin
extends AbstractPlugin

This class takes a rAmpSeq (formerly RepGen) database and for each tag in the tag table, performs the following tag-tag correlations based on the taxa distribution for each tag (1) tag-tag Pearson's correlation (2) tag-tag Spearman's correlation (3) tag-tag presence/absence correlations (4) r-squared The vectors presented to the analysis methods represent a list of taxa and the number of times the tag was seen in that taxa. The presence/absence vectors have a 1 or 0 as values in each slot.

Constructor Detail

RepGenLDAnalysisPlugin

public RepGenLDAnalysisPlugin()

RepGenLDAnalysisPlugin

public RepGenLDAnalysisPlugin(java.awt.Frame parentFrame)

RepGenLDAnalysisPlugin

public RepGenLDAnalysisPlugin(java.awt.Frame parentFrame,
                              boolean isInteractive)

Method Detail

postProcessParameters

public void postProcessParameters()

processData

public DataSet processData(DataSet input)

calculateCorrelations

public void calculateCorrelations(com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.analysis.gbs.repgen.TagCorrelationInfo> tagTagCorrelations,
                                  java.util.Map<net.maizegenetics.dna.tag.Tag,net.maizegenetics.dna.tag.TaxaDistribution> tagTaxaMap,
                                  Tag tag1,
                                  Tag tag2,
                                  kotlin.Array[] ddepths1,
                                  kotlin.Array[] depthsPrime1)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

main

public static void main(java.lang.String[] args)

getToolTipText

public java.lang.String getToolTipText()

inputDB

public java.lang.String inputDB()

Input database file with tags and taxa distribution

Returns:

org.jetbrains.dokka.NodeRenderContent@433b7b24: Input DB

inputDB

public RepGenLDAnalysisPlugin inputDB(java.lang.String value)

Set Input DB. Input database file with tags and taxa distribution

Parameters:

value - Input DB

Returns:

org.jetbrains.dokka.NodeRenderContent@52e2de5: this plugin

minTaxa

public java.lang.Integer minTaxa()

Minimum number of taxa that must be present for R-squared to be calculated.

Returns:

org.jetbrains.dokka.NodeRenderContent@39ffe4c1: Min Taxa for RSquared

minTaxa

public RepGenLDAnalysisPlugin minTaxa(java.lang.Integer value)

Set Min Taxa for RSquared. Minimum number of taxa that must be present for R-squared to be calculated.

Parameters:

value - Min Taxa for RSquared

Returns:

org.jetbrains.dokka.NodeRenderContent@4fabe868: this plugin