net.maizegenetics.analysis.data

Class SetLowDepthGenosToMissingPlugin

AbstractPlugin

net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class SetLowDepthGenosToMissingPlugin
extends AbstractPlugin

Set genotypes below a minimum depth to missing. Set each genotype in the input genotypes to missing if the underlying allelic depth is below a user- specified minimum. Input: GenotypeTable stored as a Datum within a DataSet Output: GenotypeTable stored as a Datum within a DataSet

Constructor Detail

SetLowDepthGenosToMissingPlugin

public SetLowDepthGenosToMissingPlugin()

SetLowDepthGenosToMissingPlugin

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

Method Detail

pluginDescription

public java.lang.String pluginDescription()

preProcessParameters

protected void preProcessParameters(DataSet input)

processData

public DataSet processData(DataSet input)

Main method for this plugin.

Parameters:

input - DataSet object containing the input GenotypeTable.

Returns:

org.jetbrains.dokka.NodeRenderContent@20559f11: DataSet object containing the output GenotypeTable where genotypes with depth below the specified minimum are set to missing.

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

getCitation

public java.lang.String getCitation()

runPlugin

public GenotypeTable runPlugin(GenotypeTable inputGenos)

Convenience method to run plugin with input and output GenotypeTable objects (rather than DataSets)

Parameters:

inputGenos - Input GenotypeTable.

Returns:

org.jetbrains.dokka.NodeRenderContent@72dab517: GenotypeTable where genotypes with depth below the specified minimum are set to missing.

minDepth

public java.lang.Integer minDepth()

Min Depth

Returns:

org.jetbrains.dokka.NodeRenderContent@942b299: Min Depth

minDepth

public SetLowDepthGenosToMissingPlugin minDepth(java.lang.Integer value)

Set Min Depth. Min Depth

Parameters:

value - Min Depth

Returns:

org.jetbrains.dokka.NodeRenderContent@159e40f0: this plugin