net.maizegenetics.analysis.modelfitter

Class ResamplingGWASPlugin

AbstractPlugin

net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class ResamplingGWASPlugin
extends AbstractPlugin

Constructor Detail

ResamplingGWASPlugin

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

Method Detail

preProcessParameters

protected void preProcessParameters(DataSet input)

processData

public DataSet processData(DataSet input)

pluginDescription

public java.lang.String pluginDescription()

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

setRandomSeed

public void setRandomSeed(int seed)

Initializes the random number generator with a seed. Primarily used for testing to generate reproducible results.

Parameters:

seed - the seed for the Random object

runPlugin

public TableReport runPlugin(DataSet input)

Convenience method to run plugin with one return object.

enterLimit

public java.lang.Double enterLimit()

A new term entering the model must have a p-value equal to or less than the enter limit. (Default = 1e-8)

Returns:

org.jetbrains.dokka.NodeRenderContent@1bab8b42: Enter Limit

enterLimit

public ResamplingGWASPlugin enterLimit(java.lang.Double value)

Set Enter Limit. A new term entering the model must have a p-value equal to or less than the enter limit. (Default = 1e-8)

Parameters:

value - Enter Limit

Returns:

org.jetbrains.dokka.NodeRenderContent@5da49aaa: this plugin

useResiduals

public java.lang.Boolean useResiduals()

Should new terms be tested using residuals from the prior model? The analysis runs faster using this option. (Default = true)

Returns:

org.jetbrains.dokka.NodeRenderContent@1b9b5ca6: Use residuals

useResiduals

public ResamplingGWASPlugin useResiduals(java.lang.Boolean value)

Set Use residuals. Should new terms be tested using residuals from the prior model? The analysis runs faster using this option. (Default = true)

Parameters:

value - Use residuals

Returns:

org.jetbrains.dokka.NodeRenderContent@309c919d: this plugin

numberOfIterations

public java.lang.Integer numberOfIterations()

The number of times the data should be resampled. (Default = 100)

Returns:

org.jetbrains.dokka.NodeRenderContent@77aaed57: Number of Iterations

numberOfIterations

public ResamplingGWASPlugin numberOfIterations(java.lang.Integer value)

Set Number of Iterations. The number of times the data should be resampled. (Default = 100)

Parameters:

value - Number of Iterations

Returns:

org.jetbrains.dokka.NodeRenderContent@e2258c2: this plugin

resampleProportion

public java.lang.Double resampleProportion()

The size of the sample is resample proportion times the number of observations in the complete data. For bootstrap, set this value to 1 and with replacement to true. (Default = 0.8)

Returns:

org.jetbrains.dokka.NodeRenderContent@4f9d5bcc: Resample Proportion

resampleProportion

public ResamplingGWASPlugin resampleProportion(java.lang.Double value)

Set Resample Proportion. The size of the sample is resample proportion times the number of observations in the complete data. For bootstrap, set this value to 1 and with replacement to true. (Default = 0.8)

Parameters:

value - Resample Proportion

Returns:

org.jetbrains.dokka.NodeRenderContent@1bd93bdb: this plugin

withReplacement

public java.lang.Boolean withReplacement()

Should the sample be formed by sampling with replacement? (Default = false)

Returns:

org.jetbrains.dokka.NodeRenderContent@3b39ada2: With Replacement

withReplacement

public ResamplingGWASPlugin withReplacement(java.lang.Boolean value)

Set With Replacement. Should the sample be formed by sampling with replacement? (Default = false)

Parameters:

value - With Replacement

Returns:

org.jetbrains.dokka.NodeRenderContent@2741064f: this plugin