net.maizegenetics.analysis.imputation

Class LDKNNiImputationHetV3Plugin

AbstractPlugin

net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class LDKNNiImputationHetV3Plugin
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

LDKNNiImputationHetV3Plugin

public LDKNNiImputationHetV3Plugin()

LDKNNiImputationHetV3Plugin

public LDKNNiImputationHetV3Plugin(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()

Number of sites in high LD to use in imputation

Returns:

org.jetbrains.dokka.NodeRenderContent@64ed1f19: High LD Sites

highLDSSites

public LDKNNiImputationHetV3Plugin highLDSSites(java.lang.Integer value)

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

Parameters:

value - High LD Sites

Returns:

org.jetbrains.dokka.NodeRenderContent@3f490b7c: this plugin

knnTaxa

public java.lang.Integer knnTaxa()

Number of neighbors to use in imputation

Returns:

org.jetbrains.dokka.NodeRenderContent@4e1c918a: Number of nearest neighbors

knnTaxa

public LDKNNiImputationHetV3Plugin knnTaxa(java.lang.Integer value)

Set Number of nearest neighbors. Number of neighbors to use in imputation

Parameters:

value - Number of nearest neighbors

Returns:

org.jetbrains.dokka.NodeRenderContent@3bd1413: this plugin

maxDistance

public java.lang.Integer maxDistance()

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

Returns:

org.jetbrains.dokka.NodeRenderContent@f24d6aa: Max distance between site to find LD

maxDistance

public LDKNNiImputationHetV3Plugin maxDistance(java.lang.Integer value)

Set Max distance between site to find LD. Maximum physical distance between sites to search 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@78c13ed9: this plugin

maxDistanceFromNN

public java.lang.Double maxDistanceFromNN()

Maximum distance from Nearest Neighbor

Returns:

org.jetbrains.dokka.NodeRenderContent@52fb608a: Maximum distance from Nearest Neighbor

maxDistanceFromNN

public LDKNNiImputationHetV3Plugin maxDistanceFromNN(java.lang.Double value)

Set Maximum distance from Nearest Neighbor. Maximum distance from Nearest Neighbor

Parameters:

value - Maximum distance from Nearest Neighbor

Returns:

org.jetbrains.dokka.NodeRenderContent@390deb4a: this plugin

duplicateHetsThreshold

public java.lang.Double duplicateHetsThreshold()

Threshold for defining heterozygous sites

Returns:

org.jetbrains.dokka.NodeRenderContent@1035fb47: HeterozygousThreshold

duplicateHetsThreshold

public LDKNNiImputationHetV3Plugin duplicateHetsThreshold(java.lang.Double value)

Set HeterozygousThreshold. Threshold for defining heterozygous sites

Parameters:

value - HeterozygousThreshold

Returns:

org.jetbrains.dokka.NodeRenderContent@6173286e: this plugin

automaticMajorMAF

public java.lang.Double automaticMajorMAF()

Set to Major genotype if no imputation result and MAF is below threshold

Returns:

org.jetbrains.dokka.NodeRenderContent@6885fbfa: Automatic MajorGenotype if MAF

automaticMajorMAF

public LDKNNiImputationHetV3Plugin automaticMajorMAF(java.lang.Double value)

Set Automatic MajorGenotype if MAF. Set to Major genotype if no imputation result and MAF is below threshold

Parameters:

value - Automatic MajorGenotype if MAF

Returns:

org.jetbrains.dokka.NodeRenderContent@3e840a1b: this plugin

minCoverageForDonors

public java.lang.Double minCoverageForDonors()

Minimum coverage for donor genotype and LD calculation

Returns:

org.jetbrains.dokka.NodeRenderContent@154314f: Minimum coverage for donors and LD

minCoverageForDonors

public LDKNNiImputationHetV3Plugin minCoverageForDonors(java.lang.Double value)

Set Minimum coverage for donors and LD. Minimum coverage for donor genotype and LD calculation

Parameters:

value - Minimum coverage for donors and LD

Returns:

org.jetbrains.dokka.NodeRenderContent@791c4953: this plugin

minCallBestGenoRatio

public java.lang.Double minCallBestGenoRatio()

Minimum ratio between best and second best genotype to make a call

Returns:

org.jetbrains.dokka.NodeRenderContent@3e8127a1: Minimum support ratio for best genotype

minCallBestGenoRatio

public LDKNNiImputationHetV3Plugin minCallBestGenoRatio(java.lang.Double value)

Set Minimum support ratio for best genotype. Minimum ratio between best and second best genotype to make a call

Parameters:

value - Minimum support ratio for best genotype

Returns:

org.jetbrains.dokka.NodeRenderContent@20cb26b8: this plugin

maxCores

public java.lang.Integer maxCores()

Maximum number of cores to be used for processing

Returns:

org.jetbrains.dokka.NodeRenderContent@35a5a7: Maximum number of cores for processing

maxCores

public LDKNNiImputationHetV3Plugin maxCores(java.lang.Integer value)

Set Maximum number of cores for processing. Maximum number of cores to be used for processing

Parameters:

value - Maximum number of cores for processing

Returns:

org.jetbrains.dokka.NodeRenderContent@1b783223: 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