net.maizegenetics.analysis.association

Class AbstractFixedEffectLM

net.maizegenetics.analysis.association.AbstractFixedEffectLM

All Implemented Interfaces:

FixedEffectLM

Direct Known Subclasses:

AlleleProbabilityFELM, DiscreteSitesFELM, ReferenceProbabilityFELM

public class AbstractFixedEffectLM
implements FixedEffectLM

Field Detail

myLogger

protected static org.apache.log4j.Logger myLogger

myDatum

protected Datum myDatum

myGenoPheno

protected GenotypePhenotype myGenoPheno

numberOfObservations

protected int numberOfObservations

numberOfSites

protected int numberOfSites

myDataAttributes

protected java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> myDataAttributes

myFactorAttributes

protected java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> myFactorAttributes

myCovariateAttributes

protected java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> myCovariateAttributes

siteReportBuilder

protected TableReportBuilder siteReportBuilder

alleleReportBuilder

protected TableReportBuilder alleleReportBuilder

numberOfSiteReportColumns

protected int numberOfSiteReportColumns

numberOfAlleleReportColumns

protected int numberOfAlleleReportColumns

allData

protected kotlin.Array[] allData

myCurrentSite

protected int myCurrentSite

myCurrentSiteMinimumClassSize

protected int myCurrentSiteMinimumClassSize

siteData

protected kotlin.Array[] siteData

missingObsForSite

protected OpenBitSet missingObsForSite

currentTraitName

protected java.lang.String currentTraitName

areTaxaReplicated

protected boolean areTaxaReplicated

saveToFile

protected boolean saveToFile

siteReportFilename

protected java.lang.String siteReportFilename

alleleReportFilename

protected java.lang.String alleleReportFilename

maxP

protected double maxP

myParentPlugin

protected FixedEffectLMPlugin myParentPlugin

appendAddDomEffects

protected boolean appendAddDomEffects

minClassSize

protected int minClassSize

biallelicOnly

protected boolean biallelicOnly

outputSiteStats

protected boolean outputSiteStats

siteStatsFile

protected java.lang.String siteStatsFile

permute

protected boolean permute

numberOfPermutations

protected int numberOfPermutations

minP

protected kotlin.Array[] minP

permutedData

protected java.util.List<net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix> permutedData

baseErrorSSdf

protected kotlin.Array[] baseErrorSSdf

totalcfmSSdf

protected kotlin.Array[] totalcfmSSdf

markerSSdf

protected kotlin.Array[] markerSSdf

errorSSdf

protected kotlin.Array[] errorSSdf

siteTableReportRows

protected java.util.List<kotlin.Array[]> siteTableReportRows

markerpvalueColumn

protected int markerpvalueColumn

permpvalueColumn

protected int permpvalueColumn

myModel

protected java.util.ArrayList<net.maizegenetics.stats.linearmodels.ModelEffect> myModel

G

protected DoubleMatrix G

myBaseModel

protected java.util.ArrayList<net.maizegenetics.stats.linearmodels.ModelEffect> myBaseModel

numberOfBaseEffects

protected int numberOfBaseEffects

taxaEffectNumber

protected int taxaEffectNumber

randomSeed

protected int randomSeed

useRandomSeed

protected boolean useRandomSeed

rand

protected java.util.Random rand

typeNameMap

protected static java.util.Map<net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE,java.lang.String> typeNameMap

Constructor Detail

AbstractFixedEffectLM

public AbstractFixedEffectLM(Datum dataset,
                             FixedEffectLMPlugin parentPlugin)

Method Detail

initializeReportBuilders

public void initializeReportBuilders()

solve

public void solve()

siteReport

public TableReport siteReport()

alleleReport

public TableReport alleleReport()

datumList

public java.util.List<net.maizegenetics.plugindef.Datum> datumList()

permutationTest

public void permutationTest(boolean permute,
                            int nperm)

getGenotypeAndUpdateMissing

protected void getGenotypeAndUpdateMissing(BitSet missingObsBeforeSite)

Parameters:

missingObsBeforeSite - a BitSet with bits set for observations missing in model covariates and data

getGenotypeAfterUpdatingMissing

protected void getGenotypeAfterUpdatingMissing()

updates the genotype after missingObsForSite has changed

analyzeSite

protected void analyzeSite()

siteReportColumnNames

protected java.lang.String[] siteReportColumnNames()

alleleReportColumnNames

protected java.lang.String[] alleleReportColumnNames()

baseModel

protected java.util.ArrayList<net.maizegenetics.stats.linearmodels.ModelEffect> baseModel()

createPermutedData

protected void createPermutedData()

updateReportsWithPermutationP

protected void updateReportsWithPermutationP()

taxaEffect

protected ModelEffect taxaEffect()

testTaxaReplication

protected void testTaxaReplication()

updateMinP

protected void updateMinP(BitSet missingObsBeforeSite)

maxP

public void maxP(double maxP)

siteReportFilepath

public void siteReportFilepath(java.lang.String savefile)

alleleReportFilepath

public void alleleReportFilepath(java.lang.String savefile)

biallelicOnly

public void biallelicOnly(boolean biallelic)

minimumClassSize

public void minimumClassSize(int minsize)

saveSiteStats

public void saveSiteStats(boolean siteStats)

siteStatsFile

public void siteStatsFile(java.lang.String filename)

appendAddDom

public void appendAddDom(boolean append)

setRandomSeed

public void setRandomSeed(int seed)

This method is used mainly for testing in order to generate reproducible permutation results. If the seed is not set, the current time is used to initialize the random number generator.

Parameters:

seed - the seed used to initialize the random number generator used by permutation