net.maizegenetics.analysis.association

Interface FixedEffectLM

All Known Implementing Classes:

AbstractFixedEffectLM, AlleleProbabilityFELM, DiscreteSitesFELM, ReferenceProbabilityFELM

public interface FixedEffectLM

Method Summary

Modifier and Type	Method and Description
TableReport	alleleReport()
void	alleleReportFilepath(String savefile)
void	appendAddDom(boolean append)
void	biallelicOnly(boolean biallelic)
List<Datum>	datumList()
void	initializeReportBuilders() Initializes builders for the site and allele reports.
void	maxP(double maxP)
void	minimumClassSize(int minsize)
void	permutationTest(boolean permute, int nperm)
void	saveSiteStats(boolean siteStats)
TableReport	siteReport()
void	siteReportFilepath(String savefile)
void	siteStatsFile(String filename)
void	solve() Solves the linear model

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:

the site report, which contains tests of significance for each site

alleleReport

TableReport alleleReport()

Returns:

the allele report, which contains estimates and observation numbers for each allele at each site

datumList

List<Datum> datumList()

Returns:

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(String savefile)

Parameters:

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

alleleReportFilepath

void alleleReportFilepath(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(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.