net.maizegenetics.analysis.association

Interface FixedEffectLM

All Known Implementing Classes:

AbstractFixedEffectLM, AlleleProbabilityFELM, DiscreteSitesFELM, ReferenceProbabilityFELM

public FixedEffectLM

Method Detail

initializeReportBuilders

void initializeReportBuilders()

Initializes builders for the site and allele reports. The report names and column headers for a specific analysis are created in this method.

solve

void solve()

Solves the linear model

siteReport

TableReport siteReport()

Returns:

org.jetbrains.dokka.NodeRenderContent@6f016e2e: the site report, which contains tests of significance for each site

alleleReport

TableReport alleleReport()

Returns:

org.jetbrains.dokka.NodeRenderContent@47b22415: the allele report, which contains estimates and observation numbers for each allele at each site

datumList

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

Returns:

org.jetbrains.dokka.NodeRenderContent@73557225: the site and allele reports as a list of Datum

permutationTest

void permutationTest(boolean permute,
                     int nperm)

Parameters:

permute - if true, conduct an experiment-wise permutation test

nperm - the number of permutations to be run

maxP

void maxP(double maxP)

Parameters:

maxP - test results with p > maxP will not be reported.

siteReportFilepath

void siteReportFilepath(java.lang.String savefile)

Parameters:

savefile - results will be saved to this file instead of memory

alleleReportFilepath

void alleleReportFilepath(java.lang.String savefile)

Parameters:

savefile - results will be saved to this file instead of memory

biallelicOnly

void biallelicOnly(boolean biallelic)

Parameters:

biallelic - If true, only biallelic sites will be included in the analysis

minimumClassSize

void minimumClassSize(int minsize)

Parameters:

minsize - If a genotype class has fewer than minsize observations, it will not be tested.

saveSiteStats

void saveSiteStats(boolean siteStats)

Parameters:

siteStats - If true, site statistics will be output as a file.

siteStatsFile

void siteStatsFile(java.lang.String filename)

Parameters:

filename - The filename to which the site statistics will be written

appendAddDom

void appendAddDom(boolean append)

Parameters:

append - If true, additive and dominance effects will be add to the stats report for bi-allelic loci.