net.maizegenetics.analysis.distance

Class AMatrixPlugin

AbstractPlugin

net.maizegenetics.analysis.distance.AMatrixPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class AMatrixPlugin
extends AbstractPlugin

Field Detail

myProgenyIDs

protected java.util.List<java.lang.String> myProgenyIDs

Constructor Detail

AMatrixPlugin

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

Method Detail

pluginDescription

public java.lang.String pluginDescription()

processData

public DataSet processData(DataSet input)

plinkToPed

public static java.lang.String[] plinkToPed(java.lang.String ped)

Takes a filepath to a PLINK formatted file(see below). Converts to a String[][] format where each row contains 3 columns: Individual Identifier, Paternal Identifier, Maternal Identifier This format is convenient in calculating an pedigree-based kinship (A) matrix Expected PLINK pedigree file format (.ped) Family ID Individual ID Paternal ID Maternal ID and several more fields These fields are separated by one or more whitespace characters, and each row is on its own line. For our purposes, we expect every Individual ID in the file to be unique

Parameters:

ped - filepath to a valid PLINK .ped file, or compatible file format

Returns:

org.jetbrains.dokka.NodeRenderContent@67ed3c17: A n by 3 matrix representing a pedigree as progeny,parent,parent

pedMatrix

public kotlin.Array[] pedMatrix(java.lang.String[] pedigree)

Calculates an A matrix from a pedigree (see net.maizegenetics.analysis.distance.AMatrixPlugin$plinkToPed(java.lang.String))

Parameters:

pedigree - A n by 3 matrix, where each row is of the format myProgeny, parent1, parent2, where each is its unique string identifier. Identifiers of * blank, "0" are treated as unknown parents.

Returns:

org.jetbrains.dokka.NodeRenderContent@5cd937eb: A pedigree matrix, sorted alphabetically, with one row for each non-unknown parent.

See Also:

net.maizegenetics.analysis.distance.AMatrixPlugin$plinkToPed(java.lang.String)

getNameList

public java.util.List<java.lang.String> getNameList(java.lang.String[] pedigree)

Given a pedigree in net.maizegenetics.analysis.distance.AMatrixPlugin$plinkToPed(java.lang.String) format, returns the ordered list of identifiers used as indices in the matrix returned by net.maizegenetics.analysis.distance.AMatrixPlugin$pedMatrix(Array((Array((java.lang.String))))).

Parameters:

pedigree - A n by 3 matrix, where each row is of the format myProgeny, parent1, parent2, where each is its unique string identifier. Identifiers of blank, "0" are treated as unknown parents.

Returns:

org.jetbrains.dokka.NodeRenderContent@3ca2c2f: the ordered list of identifiers used as indices in the pedigree-based A matrix.

See Also:

net.maizegenetics.analysis.distance.AMatrixPlugin$plinkToPed(java.lang.String), net.maizegenetics.analysis.distance.AMatrixPlugin$pedMatrix(Array((Array((java.lang.String)))))

pedFilename

public java.lang.String pedFilename()

Create A Matrix

Returns:

org.jetbrains.dokka.NodeRenderContent@2d2bcc48: Ped Filename

pedFilename

public AMatrixPlugin pedFilename(java.lang.String value)

Set Ped Filename. Create A Matrix

Parameters:

value - Ped Filename

Returns:

org.jetbrains.dokka.NodeRenderContent@2328507e: this plugin

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

getCitation

public java.lang.String getCitation()