net.maizegenetics.analysis.imputation

Class LDKNNiImputationPlugin

AbstractPlugin

net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class LDKNNiImputationPlugin
extends AbstractPlugin

This imputation algorithm uses LD to identify good predictors for each SNP, and then uses the high LD SNPs to identify K- Nearest Neighbors. The genotype is called with a weighted mode of the KNNs.

Constructor Detail

LDKNNiImputationPlugin

public LDKNNiImputationPlugin()

LDKNNiImputationPlugin

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

Method Detail

preProcessParameters

protected void preProcessParameters(DataSet input)

processData

public DataSet processData(DataSet input)

getCitation

public java.lang.String getCitation()

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

main

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

runPlugin

public GenotypeTable runPlugin(DataSet input)

Convenience method to run plugin with one return object.

highLDSSites

public java.lang.Integer highLDSSites()

Maximum number of sites in high LD to use in imputation

Returns:

org.jetbrains.dokka.NodeRenderContent@77c43367: High LD Sites

highLDSSites

public LDKNNiImputationPlugin highLDSSites(java.lang.Integer value)

Set High LD Sites. Maximum number of sites in high LD to use in imputation

Parameters:

value - High LD Sites

Returns:

org.jetbrains.dokka.NodeRenderContent@6ba79e18: this plugin

knnTaxa

public java.lang.Integer knnTaxa()

Maximum number of neighbours to use in imputation

Returns:

org.jetbrains.dokka.NodeRenderContent@6f47d995: Number of nearest neighbors

knnTaxa

public LDKNNiImputationPlugin knnTaxa(java.lang.Integer value)

Set Number of nearest neighbors. Maximum number of neighbours to use in imputation

Parameters:

value - Number of nearest neighbors

Returns:

org.jetbrains.dokka.NodeRenderContent@4d3f1784: this plugin

maxDistance

public java.lang.Integer maxDistance()

Maximum physical distance between sites to look for LD (-1 for no distance cutoff - unlinked chromosomes will be tested)

Returns:

org.jetbrains.dokka.NodeRenderContent@1bb64a4f: Max distance between site to find LD

maxDistance

public LDKNNiImputationPlugin maxDistance(java.lang.Integer value)

Set Max distance between site to find LD. Maximum physical distance between sites to look for LD (-1 for no distance cutoff - unlinked chromosomes will be tested)

Parameters:

value - Max distance between site to find LD

Returns:

org.jetbrains.dokka.NodeRenderContent@4cb6507f: this plugin

dist

public static kotlin.Array[] dist(kotlin.Array[] b1,
                                  kotlin.Array[] b2,
                                  int min)

Alternative to current IBS distance measure AA <> AA = 0 Aa <> Aa = 0 distance (normal IBS distance this is 0.5) AA <> aa = 1 distance