net.maizegenetics.analysis.association

Class EqtlAssociationPlugin

AbstractPlugin

net.maizegenetics.analysis.association.EqtlAssociationPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class EqtlAssociationPlugin
extends AbstractPlugin

Constructor Detail

EqtlAssociationPlugin

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

Method Detail

processData

public DataSet processData(DataSet input)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

runPlugin

public TableReport runPlugin(DataSet input)

Convenience method to run plugin with one return object.

maxPValue

public java.lang.Double maxPValue()

The maximum p-value that will be output by the analysis.

Returns:

org.jetbrains.dokka.NodeRenderContent@382ecbfe: MaxPValue

maxPValue

public EqtlAssociationPlugin maxPValue(java.lang.Double value)

Set MaxPValue. The maximum p-value that will be output by the analysis.

Parameters:

value - MaxPValue

Returns:

org.jetbrains.dokka.NodeRenderContent@7b5e01f: this plugin

additiveOnlyModel

public java.lang.Boolean additiveOnlyModel()

Should an additive only model be fit? If true, an additive model will be fit. If false, an additive + dominance model will be fit. Default = false.

Returns:

org.jetbrains.dokka.NodeRenderContent@6c26c78: Additive Only Model

additiveOnlyModel

public EqtlAssociationPlugin additiveOnlyModel(java.lang.Boolean value)

Set Additive Only Model. Should an additive only model be fit? If true, an additive model will be fit. If false, an additive + dominance model will be fit. Default = false.

Parameters:

value - Additive Only Model

Returns:

org.jetbrains.dokka.NodeRenderContent@9e5513a: this plugin

genotypeComponent

public net.maizegenetics.dna.snp.GenotypeTable.GENOTYPE_TABLE_COMPONENT genotypeComponent()

If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.

Returns:

org.jetbrains.dokka.NodeRenderContent@47da1ac3: Genotype Component

genotypeComponent

public EqtlAssociationPlugin genotypeComponent(net.maizegenetics.dna.snp.GenotypeTable.GENOTYPE_TABLE_COMPONENT value)

Set Genotype Component. If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.

Parameters:

value - Genotype Component

Returns:

org.jetbrains.dokka.NodeRenderContent@6f47bf3f: this plugin

writeToFile

public java.lang.Boolean writeToFile()

Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will NOT be saved to the data tree. Default = false.

Returns:

org.jetbrains.dokka.NodeRenderContent@7a73bf03: Write to file

writeToFile

public EqtlAssociationPlugin writeToFile(java.lang.Boolean value)

Set Write to file. Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will NOT be saved to the data tree. Default = false.

Parameters:

value - Write to file

Returns:

org.jetbrains.dokka.NodeRenderContent@593c4df6: this plugin

outputFile

public java.lang.String outputFile()

The name of the file to which these results will be saved.

Returns:

org.jetbrains.dokka.NodeRenderContent@4ea75810: Output File

outputFile

public EqtlAssociationPlugin outputFile(java.lang.String value)

Set Output File. The name of the file to which these results will be saved.

Parameters:

value - Output File

Returns:

org.jetbrains.dokka.NodeRenderContent@1c4ba8bc: this plugin

getCitation

public java.lang.String getCitation()