org.metaqtl
Class MetaQtlAnalysis

java.lang.Object
  org.metaqtl.MetaQtlAnalysis

public class MetaQtlAnalysis
extends java.lang.Object

A QTL meta analysis consists in a clustering of QTL positions over chromosomes for different group of traits. The a MetaQtlAnalysis object is just a bundle of chromosomes in each of which the result of the meta analysis is stored.

Field Summary

java.lang.String[]	chromNames The names of the chromosomes.
int	nchr The number of chromosomes on which the meta-analysis has been performed.
Qtl[][]	qtlByChrom The matrix of qtl by chromosome
MetaQtlResult[][]	resultByChrom The matrix of results where the rows are the chromosomes.

Constructor Summary

MetaQtlAnalysis(int nchr)
Creates a new instance of a MetaQtlAnalysis

Method Summary

MetaQtlModel	getBestModel(int criterion) This methods returns the best models for each criterion defined to select the optimal number of clusters per chromosome per trait.
int	getChromIdx(java.lang.String chrom)
Qtl[]	getMetaQtl(java.lang.String chrom, java.lang.String trait, int k) Returns the meta Qtl for the given chromosome indice cidx, the given trait name trait and the given number of clusters k.
MetaQtlResult	getResult(int chromIdx, java.lang.String trait) Returns the result for the given trait name or null if not found.
MetaQtlResult	getResult(java.lang.String chrom) Returns the first result for the given chromosome.
MetaQtlResult	getResult(java.lang.String chrom, java.lang.String trait) Returns the result for the given trait name or null if not found.
MetaQtlResult[]	getResults(java.lang.String chromName)
int	getTraitIdx(int chromIdx, java.lang.String trait)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

nchr

public int nchr

The number of chromosomes on which the meta-analysis has been performed.

chromNames

public java.lang.String[] chromNames

The names of the chromosomes.

qtlByChrom

public Qtl[][] qtlByChrom

The matrix of qtl by chromosome

resultByChrom

public MetaQtlResult[][] resultByChrom

The matrix of results where the rows are the chromosomes.

Constructor Detail

MetaQtlAnalysis

public MetaQtlAnalysis(int nchr)

Creates a new instance of a MetaQtlAnalysis

Parameters:

nchr - the number of chromosomes on which the meta-analysis has been performed.

Method Detail

getResult

public MetaQtlResult getResult(java.lang.String chrom,
                               java.lang.String trait)

Returns the result for the given trait name or null if not found.

Parameters:

trait - the name of the trait for which the result is asked.

Returns:

the result or null if not found.

getResult

public MetaQtlResult getResult(java.lang.String chrom)

Returns the first result for the given chromosome.

Returns:

the result or null if not found.

getResult

public MetaQtlResult getResult(int chromIdx,
                               java.lang.String trait)

Returns the result for the given trait name or null if not found.

Parameters:

trait - the name of the trait for which the result is asked.

Returns:

the result or null if not found.

getChromIdx

public int getChromIdx(java.lang.String chrom)

Returns:

getTraitIdx

public int getTraitIdx(int chromIdx,
                       java.lang.String trait)

Returns:

getMetaQtl

public Qtl[] getMetaQtl(java.lang.String chrom,
                        java.lang.String trait,
                        int k)

Returns the meta Qtl for the given chromosome indice cidx, the given trait name trait and the given number of clusters k.

Parameters:

cidx -

trait -

k -

getBestModel

public MetaQtlModel getBestModel(int criterion)

This methods returns the best models for each criterion defined to select the optimal number of clusters per chromosome per trait.

Returns:

getResults

public MetaQtlResult[] getResults(java.lang.String chromName)