net.maizegenetics.analysis.imputation

Class LDKNNiImputationHetV2Plugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin

All Implemented Interfaces:

Runnable, Plugin, PluginListener, ProgressListener

public class LDKNNiImputationHetV2Plugin
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.

Author:

Daniel Money (Developer and developed the algorithm), Ed Buckler (assisted in conversion to TASSEL)

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
LDKNNiImputationHetV2Plugin()
LDKNNiImputationHetV2Plugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
Double	automaticMajorMAF() Set to Major genotype if no imputation result and MAF is below threshold
LDKNNiImputationHetV2Plugin	automaticMajorMAF(Double value) Set Automatic MajorGenotype if MAF.
static double[]	dist(byte[] b1, byte[] 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
Double	duplicateHetsThreshold() Threshold for defining heterozygous sites
LDKNNiImputationHetV2Plugin	duplicateHetsThreshold(Double value) Set HeterozygousThreshold.
String	getButtonName() Button name for this plugin to be used in buttons, etc.
String	getCitation() Returns Citation for this plugin.
ImageIcon	getIcon() Icon for this plugin to be used in buttons, etc.
String	getToolTipText() Tool Tip Text for this plugin
Integer	highLDSSites() Number of sites in high LD to use in imputation
LDKNNiImputationHetV2Plugin	highLDSSites(Integer value) Set High LD Sites.
Integer	knnTaxa() Number of neighbors to use in imputation
LDKNNiImputationHetV2Plugin	knnTaxa(Integer value) Set Number of nearest neighbors.
static void	main(String[] args)
Integer	maxCores() Maximum number of cores to be used for processing
LDKNNiImputationHetV2Plugin	maxCores(Integer value) Set Maximum number of cores for processing.
Integer	maxDistance() Maximum physical distance between sites to search for LD (-1 for no distance cutoff - unlinked chromosomes will be tested)
LDKNNiImputationHetV2Plugin	maxDistance(Integer value) Set Max distance between site to find LD.
Double	maxDistanceFromNN() Maximum distance from Nearest Neighbor
LDKNNiImputationHetV2Plugin	maxDistanceFromNN(Double value) Set Maximum distance from Nearest Neighbor.
Double	minCallBestGenoRatio() Minimum ratio between best and second best genotype to make a call
LDKNNiImputationHetV2Plugin	minCallBestGenoRatio(Double value) Set Minimum support ratio for best genotype.
Double	minCoverageForDonors() Minimum coverage for donor genotype and LD calculation
LDKNNiImputationHetV2Plugin	minCoverageForDonors(Double value) Set Minimum coverage for donors and LD.
DataSet	processData(DataSet input) For the new Generic Plugin Parameter design, performFunction() will automatically call this.
GenotypeTable	runPlugin(DataSet input) Convenience method to run plugin with one return object.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, pluginUserManualURL, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParameters, setParametersToDefault, setThreaded, trace, wasCancelled

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.maizegenetics.plugindef.Plugin

getPluginInstance, getPluginInstance, isPlugin

Constructor Detail

LDKNNiImputationHetV2Plugin

public LDKNNiImputationHetV2Plugin()

LDKNNiImputationHetV2Plugin

public LDKNNiImputationHetV2Plugin(Frame parentFrame,
                                   boolean isInteractive)

Method Detail

processData

public DataSet processData(DataSet input)

Description copied from interface: Plugin

For the new Generic Plugin Parameter design, performFunction() will automatically call this. Therefore, coders of Plugins should override this instead of performFunction().

Specified by:

processData in interface Plugin

Overrides:

processData in class AbstractPlugin

Parameters:

input - input

Returns:

resulting data set or null.

getCitation

public String getCitation()

Description copied from interface: Plugin

Returns Citation for this plugin.

Specified by:

getCitation in interface Plugin

Overrides:

getCitation in class AbstractPlugin

Returns:

Citation

getIcon

public ImageIcon getIcon()

Description copied from interface: Plugin

Icon for this plugin to be used in buttons, etc.

Returns:

ImageIcon

getButtonName

public String getButtonName()

Description copied from interface: Plugin

Button name for this plugin to be used in buttons, etc.

Returns:

String

getToolTipText

public String getToolTipText()

Description copied from interface: Plugin

Tool Tip Text for this plugin

Returns:

String

main

public static void main(String[] args)

runPlugin

public GenotypeTable runPlugin(DataSet input)

Convenience method to run plugin with one return object.

highLDSSites

public Integer highLDSSites()

Number of sites in high LD to use in imputation

Returns:

High LD Sites

highLDSSites

public LDKNNiImputationHetV2Plugin highLDSSites(Integer value)

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

Parameters:

value - High LD Sites

Returns:

this plugin

knnTaxa

public Integer knnTaxa()

Number of neighbors to use in imputation

Returns:

Number of nearest neighbors

knnTaxa

public LDKNNiImputationHetV2Plugin knnTaxa(Integer value)

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

Parameters:

value - Number of nearest neighbors

Returns:

this plugin

maxDistance

public Integer maxDistance()

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

Returns:

Max distance between site to find LD

maxDistance

public LDKNNiImputationHetV2Plugin maxDistance(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:

this plugin

maxDistanceFromNN

public Double maxDistanceFromNN()

Maximum distance from Nearest Neighbor

Returns:

Maximum distance from Nearest Neighbor

maxDistanceFromNN

public LDKNNiImputationHetV2Plugin maxDistanceFromNN(Double value)

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

Parameters:

value - Maximum distance from Nearest Neighbor

Returns:

this plugin

duplicateHetsThreshold

public Double duplicateHetsThreshold()

Threshold for defining heterozygous sites

Returns:

HeterozygousThreshold

duplicateHetsThreshold

public LDKNNiImputationHetV2Plugin duplicateHetsThreshold(Double value)

Set HeterozygousThreshold. Threshold for defining heterozygous sites

Parameters:

value - HeterozygousThreshold

Returns:

this plugin

automaticMajorMAF

public Double automaticMajorMAF()

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

Returns:

Automatic MajorGenotype if MAF

automaticMajorMAF

public LDKNNiImputationHetV2Plugin automaticMajorMAF(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:

this plugin

minCoverageForDonors

public Double minCoverageForDonors()

Minimum coverage for donor genotype and LD calculation

Returns:

Minimum coverage for donors and LD

minCoverageForDonors

public LDKNNiImputationHetV2Plugin minCoverageForDonors(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:

this plugin

minCallBestGenoRatio

public Double minCallBestGenoRatio()

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

Returns:

Minimum support ratio for best genotype

minCallBestGenoRatio

public LDKNNiImputationHetV2Plugin minCallBestGenoRatio(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:

this plugin

maxCores

public Integer maxCores()

Maximum number of cores to be used for processing

Returns:

Maximum number of cores for processing

maxCores

public LDKNNiImputationHetV2Plugin maxCores(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:

this plugin

dist

public static double[] dist(byte[] b1,
                            byte[] 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