net.maizegenetics.analysis.association

Class GenomicSelectionPlugin

AbstractPlugin

net.maizegenetics.analysis.association.GenomicSelectionPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class GenomicSelectionPlugin
extends AbstractPlugin

Constructor Detail

GenomicSelectionPlugin

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

Method Detail

processData

public DataSet processData(DataSet input)

processDataforPrediction

public DataSet processDataforPrediction(Phenotype myPhenotype,
                                        DistanceMatrix kinshipMatrix,
                                        java.lang.String inputPhenotypeName)

processDataforCrossValidation

public DataSet processDataforCrossValidation(Phenotype reducedPheno,
                                             DistanceMatrix kinshipOriginal,
                                             java.lang.String inputPhenotypeName)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

pluginDescription

public java.lang.String pluginDescription()

getCitation

public java.lang.String getCitation()

runPlugin

public DataSet runPlugin(DataSet input)

Convenience method to run plugin with one return object.

Parameters:

input -

performCrossValidation

public java.lang.Boolean performCrossValidation()

Perform cross-validation: True or False

Returns:

org.jetbrains.dokka.NodeRenderContent@6434fe32: Perform cross-validation

performCrossValidation

public GenomicSelectionPlugin performCrossValidation(java.lang.Boolean value)

Set Perform cross-validation. Perform cross-validation: True or False

Parameters:

value - Perform cross-validation

Returns:

org.jetbrains.dokka.NodeRenderContent@6abd2e45: this plugin

kFolds

public java.lang.Integer kFolds()

Number of folds to use for k-fold cross-validation (default = 5)

Returns:

org.jetbrains.dokka.NodeRenderContent@179a570c: Number of folds

kFolds

public GenomicSelectionPlugin kFolds(java.lang.Integer value)

Set Number of folds. Number of folds to use for k-fold cross-validation (default = 5)

Parameters:

value - Number of folds

Returns:

org.jetbrains.dokka.NodeRenderContent@531acd1d: this plugin

nIterations

public java.lang.Integer nIterations()

Number of iterations when running k-fold cross-validation (default = 20)

Returns:

org.jetbrains.dokka.NodeRenderContent@109c6c22: Number of iterations

nIterations

public GenomicSelectionPlugin nIterations(java.lang.Integer value)

Set Number of iterations. Number of iterations when running k-fold cross-validation (default = 20)

Parameters:

value - Number of iterations

Returns:

org.jetbrains.dokka.NodeRenderContent@13d0a772: this plugin