org.metaqtl
Class MetaQtlAnalysis

java.lang.Object
  extended by 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)