net.maizegenetics.phenotype

Class GenotypePhenotype

net.maizegenetics.phenotype.GenotypePhenotype

All Implemented Interfaces:

TableReport

public class GenotypePhenotype
implements TableReport

This class holds phenotypes and genotypes for a set of Taxa.

Method Detail

genotypeTable

public GenotypeTable genotypeTable()

Returns:

org.jetbrains.dokka.NodeRenderContent@3cf516f7: the GenotypeTable used by this object

phenotype

public Phenotype phenotype()

Returns:

org.jetbrains.dokka.NodeRenderContent@251c9e82: the Phenotype used by this object

areGenotypeValuesDiscrete

public boolean areGenotypeValuesDiscrete()

Returns:

org.jetbrains.dokka.NodeRenderContent@2148e4bf: true if genotypes are discrete (nucleotides), false if the genotypes are numeric The GenotypeTable backing this object may hold both types of data. The boolean indicates which is to be used in an analysis.

areTaxaReplicated

public boolean areTaxaReplicated()

Returns:

org.jetbrains.dokka.NodeRenderContent@1943001: true if taxa are replicated (more observations than taxa), false otherwise

getStringGenotype

public java.lang.String[] getStringGenotype(int site)

Parameters:

site - the site in the GenotypeTable

Returns:

org.jetbrains.dokka.NodeRenderContent@15c2cc6a: the genotypes corresponding to every row of the phenotype table as String values

genotype

public byte genotype(int obs,
                     int site)

Parameters:

obs - an observation number

site - a site

Returns:

org.jetbrains.dokka.NodeRenderContent@54ebb8de: the byte value of the genotype for this observation at this site

isHeterozygous

public boolean isHeterozygous(int obs,
                              int site)

genotypeAllTaxa

public kotlin.Array[] genotypeAllTaxa(int site)

Parameters:

site - the site in the GenotypeTable

Returns:

org.jetbrains.dokka.NodeRenderContent@32e0c3e0: the genotypes corresponding to every row of the phenotype table as byte values

alleleProbsOfType

public kotlin.Array[] alleleProbsOfType(net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE type,
                                        int site)

referenceProb

public kotlin.Array[] referenceProb(int site)

getTableColumnNames

public java.lang.Object[] getTableColumnNames()

getTableTitle

public java.lang.String getTableTitle()

getColumnCount

public int getColumnCount()

getRowCount

public long getRowCount()

getElementCount

public long getElementCount()

getRow

public java.lang.Object[] getRow(long row)

getValueAt

public java.lang.Object getValueAt(long row,
                                   int col)

numberOfObservations

public int numberOfObservations()

Returns:

org.jetbrains.dokka.NodeRenderContent@12d4e985: the number of observations in this GenotypePhenotype, equivalent to phenotype().numberOfObservations()