public class FixedEffectLMPlugin
extends AbstractPlugin
public FixedEffectLMPlugin(java.awt.Frame parentFrame,
boolean isInteractive)
public java.lang.String getButtonName()
public javax.swing.ImageIcon getIcon()
public java.lang.String getToolTipText()
protected void preProcessParameters(DataSet data)
public void updateProgress(int percent)
public void setOutputFile(java.lang.String name)
public void setMaxP(double maxp)
public void setPermute(boolean permute)
public void setNumberOfPermutations(int nperm)
public java.lang.Boolean phenotypeOnly()
Should the phenotype be analyzed with no markers and BLUEs generated? (BLUE = best linear unbiased estimate)
public FixedEffectLMPlugin phenotypeOnly(java.lang.Boolean value)
Set Analyze Phenotype Only. Should the phenotype be analyzed with no markers and BLUEs generated? (BLUE = best linear unbiased estimate)
value - Analyze Phenotype Onlypublic java.lang.Boolean saveAsFile()
Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will NOT be saved to the data tree. Default = false.
public FixedEffectLMPlugin saveAsFile(java.lang.Boolean value)
Set Save to file. Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will NOT be saved to the data tree. Default = false.
value - Save to filepublic java.lang.String siteReportFilename()
The name of the file to which these results will be saved.
public FixedEffectLMPlugin siteReportFilename(java.lang.String value)
Set Statistics File. The name of the file to which these results will be saved.
value - Statistics Filepublic java.lang.String alleleReportFilename()
The name of the file to which these results will be saved.
public FixedEffectLMPlugin alleleReportFilename(java.lang.String value)
Set Genotype Effect File. The name of the file to which these results will be saved.
value - Genotype Effect Filepublic java.lang.Double maxPvalue()
Only results with p <= maxPvalue will be reported. Default = 1.0.
public FixedEffectLMPlugin maxPvalue(java.lang.Double value)
Set max P value. Only results with p <= maxPvalue will be reported. Default = 1.0.
value - max P valuepublic java.lang.Boolean permute()
Should a permutation analysis be run? The permutation analysis controls the experiment-wise error rate for individual phenotypes.
public FixedEffectLMPlugin permute(java.lang.Boolean value)
Set Run Permutations. Should a permutation analysis be run? The permutation analysis controls the experiment-wise error rate for individual phenotypes.
value - Run Permutationspublic java.lang.Integer numberOfPermutations()
The number of permutations to be run for the permutation analysis.
public FixedEffectLMPlugin numberOfPermutations(java.lang.Integer value)
Set Number of Permutations. The number of permutations to be run for the permutation analysis.
value - Number of Permutationspublic net.maizegenetics.dna.snp.GenotypeTable.GENOTYPE_TABLE_COMPONENT genotypeTable()
If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
public FixedEffectLMPlugin genotypeTable(net.maizegenetics.dna.snp.GenotypeTable.GENOTYPE_TABLE_COMPONENT value)
Set Genotype Component. If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
value - Genotype Componentpublic java.lang.Integer minClassSize()
The minimum acceptable genotype class size. Genotypes in a class with a smaller size will be set to missing.
public FixedEffectLMPlugin minClassSize(java.lang.Integer value)
Set Minimum Class Size. The minimum acceptable genotype class size. Genotypes in a class with a smaller size will be set to missing.
value - Minimum Class Sizepublic java.lang.Boolean biallelicOnly()
Only test sites that are bi-allelic. The alternative is to test sites with two or more alleles.
public FixedEffectLMPlugin biallelicOnly(java.lang.Boolean value)
Set Bi-Allelic Sites Only. Only test sites that are bi-allelic. The alternative is to test sites with two or more alleles.
value - Bi-Allelic Sites Onlypublic java.lang.Boolean siteStatsOutput()
Generate an output dataset with only p-val, F statistic, and number of obs per site for all sites.
public FixedEffectLMPlugin siteStatsOutput(java.lang.Boolean value)
Set Output Site Stats. Generate an output dataset with only p-val, F statistic, and number of obs per site for all sites.
value - Output Site Statspublic java.lang.String siteStatFilename()
Site Stat File
public FixedEffectLMPlugin siteStatFilename(java.lang.String value)
Set Site Stat File. Site Stat File
value - Site Stat Filepublic java.lang.Boolean appendAddDom()
If true, additive and dominance effect estimates will be added to the stats report for bi-allelic sites only. The effect will only be estimated when the data source is genotype (not a probability). The additive effect will always be non-negative.
public FixedEffectLMPlugin appendAddDom(java.lang.Boolean value)
Set Append Effect Estimates to Stats. If true, additive and dominance effect estimates will be added to the stats report for bi-allelic sites only. The effect will only be estimated when the data source is genotype (not a probability). The additive effect will always be non-negative.
value - Append Effect Estimates to Statspublic java.lang.String bluesReportFilename()
Name of file to which BLUEs values will be saved
public FixedEffectLMPlugin bluesReportFilename(java.lang.String value)
Set BLUEs File. Name of file to which BLUEs values will be saved
value - BLUEs Filepublic java.lang.String anovaReportFilename()
Name of file to which ANOVA report will be saved
public FixedEffectLMPlugin anovaReportFilename(java.lang.String value)
Set ANOVA File. Name of file to which ANOVA report will be saved
value - ANOVA File