net.maizegenetics.analysis.imputation

Class FSFHapImputationPlugin

AbstractPlugin

net.maizegenetics.analysis.imputation.FSFHapImputationPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class FSFHapImputationPlugin
extends AbstractPlugin

Constructor Detail

FSFHapImputationPlugin

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

Method Detail

getCitation

public java.lang.String getCitation()

pluginDescription

public java.lang.String pluginDescription()

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 GenotypeTable runPlugin(DataSet input)

Convenience method to run plugin with one return object.

pedigrees

public java.lang.String pedigrees()

the pedigree file name

Returns:

org.jetbrains.dokka.NodeRenderContent@7bc7a782: Pedigrees

pedigrees

public FSFHapImputationPlugin pedigrees(java.lang.String value)

Set Pedigrees. the pedigree file name

Parameters:

value - Pedigrees

Returns:

org.jetbrains.dokka.NodeRenderContent@6ccf7561: this plugin

cluster

public java.lang.Boolean cluster()

use the cluster algorithm

Returns:

org.jetbrains.dokka.NodeRenderContent@31342daf: Cluster

cluster

public FSFHapImputationPlugin cluster(java.lang.Boolean value)

Set Cluster. use the cluster algorithm

Parameters:

value - Cluster

Returns:

org.jetbrains.dokka.NodeRenderContent@79a54b28: this plugin

windowLD

public java.lang.Boolean windowLD()

use the windowLD algorithm

Returns:

org.jetbrains.dokka.NodeRenderContent@3f180829: Window L D

windowLD

public FSFHapImputationPlugin windowLD(java.lang.Boolean value)

Set Window L D. use the windowLD algorithm

Parameters:

value - Window L D

Returns:

org.jetbrains.dokka.NodeRenderContent@286b16d6: this plugin

bc

public java.lang.Boolean bc()

use the single backcross algorithm

Returns:

org.jetbrains.dokka.NodeRenderContent@38221f21: Bc

bc

public FSFHapImputationPlugin bc(java.lang.Boolean value)

Set Bc. use the single backcross algorithm

Parameters:

value - Bc

Returns:

org.jetbrains.dokka.NodeRenderContent@6b8def06: this plugin

multbc

public java.lang.Boolean multbc()

use the multiple backcross algorithm

Returns:

org.jetbrains.dokka.NodeRenderContent@142bfb1e: Multbc

multbc

public FSFHapImputationPlugin multbc(java.lang.Boolean value)

Set Multbc. use the multiple backcross algorithm

Parameters:

value - Multbc

Returns:

org.jetbrains.dokka.NodeRenderContent@648692eb: this plugin

minMaf

public java.lang.Double minMaf()

filter out sites with less than minimumMinorAlleleFrequency

Returns:

org.jetbrains.dokka.NodeRenderContent@4c75424d: Min Maf

minMaf

public FSFHapImputationPlugin minMaf(java.lang.Double value)

Set Min Maf. filter out sites with less than minimumMinorAlleleFrequency

Parameters:

value - Min Maf

Returns:

org.jetbrains.dokka.NodeRenderContent@4884711a: this plugin

window

public java.lang.Integer window()

filter out sites with less than minimumMinorAlleleFrequency

Returns:

org.jetbrains.dokka.NodeRenderContent@3bc901f: Window

window

public FSFHapImputationPlugin window(java.lang.Integer value)

Set Window. filter out sites with less than minimumMinorAlleleFrequency

Parameters:

value - Window

Returns:

org.jetbrains.dokka.NodeRenderContent@537d4b49: this plugin

minR

public java.lang.Double minR()

filter out sites not correlated with neighboring sites

Returns:

org.jetbrains.dokka.NodeRenderContent@357c1c41: Min R

minR

public FSFHapImputationPlugin minR(java.lang.Double value)

Set Min R. filter out sites not correlated with neighboring sites

Parameters:

value - Min R

Returns:

org.jetbrains.dokka.NodeRenderContent@5e9ba755: this plugin

maxMissing

public java.lang.Double maxMissing()

filter out sites with proportion missing > maxMissing

Returns:

org.jetbrains.dokka.NodeRenderContent@3940f8f1: Max Missing

maxMissing

public FSFHapImputationPlugin maxMissing(java.lang.Double value)

Set Max Missing. filter out sites with proportion missing > maxMissing

Parameters:

value - Max Missing

Returns:

org.jetbrains.dokka.NodeRenderContent@5ecb93: this plugin

nohets

public java.lang.Boolean nohets()

delete heterozygous calls before imputing

Returns:

org.jetbrains.dokka.NodeRenderContent@559551cd: Nohets

nohets

public FSFHapImputationPlugin nohets(java.lang.Boolean value)

Set Nohets. delete heterozygous calls before imputing

Parameters:

value - Nohets

Returns:

org.jetbrains.dokka.NodeRenderContent@56b7e525: this plugin

maxDiff

public java.lang.Integer maxDiff()

use to decide if two haplotypes are equivalent

Returns:

org.jetbrains.dokka.NodeRenderContent@688e1872: Max Diff

maxDiff

public FSFHapImputationPlugin maxDiff(java.lang.Integer value)

Set Max Diff. use to decide if two haplotypes are equivalent

Parameters:

value - Max Diff

Returns:

org.jetbrains.dokka.NodeRenderContent@1efa54a3: this plugin

minHap

public java.lang.Integer minHap()

haplotype must be observed at least this often

Returns:

org.jetbrains.dokka.NodeRenderContent@619e6588: Min Hap

minHap

public FSFHapImputationPlugin minHap(java.lang.Integer value)

Set Min Hap. haplotype must be observed at least this often

Parameters:

value - Min Hap

Returns:

org.jetbrains.dokka.NodeRenderContent@8e92a53: this plugin

overlap

public java.lang.Integer overlap()

overlap between adjacent windows

Returns:

org.jetbrains.dokka.NodeRenderContent@103ceeb4: Overlap

overlap

public FSFHapImputationPlugin overlap(java.lang.Integer value)

Set Overlap. overlap between adjacent windows

Parameters:

value - Overlap

Returns:

org.jetbrains.dokka.NodeRenderContent@5c2fef5c: this plugin

fillgaps

public java.lang.Boolean fillgaps()

replace missing values with flanking values if equal

Returns:

org.jetbrains.dokka.NodeRenderContent@4e8f6374: Fillgaps

fillgaps

public FSFHapImputationPlugin fillgaps(java.lang.Boolean value)

Set Fillgaps. replace missing values with flanking values if equal

Parameters:

value - Fillgaps

Returns:

org.jetbrains.dokka.NodeRenderContent@f757344: this plugin

phet

public java.lang.Double phet()

proportion of sites that are heterozygous

Returns:

org.jetbrains.dokka.NodeRenderContent@784b6550: Phet

phet

public FSFHapImputationPlugin phet(java.lang.Double value)

Set Phet. proportion of sites that are heterozygous

Parameters:

value - Phet

Returns:

org.jetbrains.dokka.NodeRenderContent@5bbd200a: this plugin

merge

public java.lang.Boolean merge()

merge families and chromosomes

Returns:

org.jetbrains.dokka.NodeRenderContent@6e9c7cca: Merge

merge

public FSFHapImputationPlugin merge(java.lang.Boolean value)

Set Merge. merge families and chromosomes

Parameters:

value - Merge

Returns:

org.jetbrains.dokka.NodeRenderContent@4a57dd0e: this plugin

outParents

public java.lang.Boolean outParents()

replace missing values with flanking values if equal

Returns:

org.jetbrains.dokka.NodeRenderContent@699540f1: Out Parents

outParents

public FSFHapImputationPlugin outParents(java.lang.Boolean value)

Set Out Parents. replace missing values with flanking values if equal

Parameters:

value - Out Parents

Returns:

org.jetbrains.dokka.NodeRenderContent@5b9a80b9: this plugin

outNuc

public java.lang.Boolean outNuc()

replace missing values with flanking values if equal

Returns:

org.jetbrains.dokka.NodeRenderContent@56edcd2c: Out Nuc

outNuc

public FSFHapImputationPlugin outNuc(java.lang.Boolean value)

Set Out Nuc. replace missing values with flanking values if equal

Parameters:

value - Out Nuc

Returns:

org.jetbrains.dokka.NodeRenderContent@2226c552: this plugin

outIUPAC

public java.lang.Boolean outIUPAC()

use IUPAC ambiguity codes for output

Returns:

org.jetbrains.dokka.NodeRenderContent@61778b2f: Out I U P A C

outIUPAC

public FSFHapImputationPlugin outIUPAC(java.lang.Boolean value)

Set Out I U P A C. use IUPAC ambiguity codes for output

Parameters:

value - Out I U P A C

Returns:

org.jetbrains.dokka.NodeRenderContent@6ee750f0: this plugin