org.metaqtl
Class MetaQtlResult

java.lang.Object
  extended by org.metaqtl.MetaQtlResult

public class MetaQtlResult
extends java.lang.Object

A MetaQtlResult is used to store the results of a QTL meta analysis which has been performed for a given trait group on a given chromosome.


Field Summary
 EMResult[] clusterings
          The meta qtl clusterings.
 int nmqc
          The number of meta qtl clusterings.
 int nqtl
          The number of QTL
 int[] qtlIdx
          The indices of QTL which are implied in the analysis.
 double[] sd
          The QTL position standard deviations.
 java.lang.String trait
          The name of the trait.
 Tree tree
          The qtl tree
 double[] x
          The QTL positions.
 
Constructor Summary
MetaQtlResult()
           
MetaQtlResult(java.lang.String trait, int qtlNumber)
           
 
Method Summary
 EMResult getBestClustering(int criterion)
          This methods returns the best models for each criterion defined to select the optimal number of clusters per trait.
 EMResult getClustering(int k)
          Returns the Qtl clustering result with k clusters.
 double[] getCritDelta(java.lang.String criterion, int[] K)
           
 java.util.Iterator getCriteria()
           
 double[] getCritValues(java.lang.String criterion, int[] K)
           
 double[] getCritWeights(java.lang.String criterion, int[] K)
           
 int[] getKValues()
           
 Qtl[] getMetaQtl(int k)
           
 Tree getQtlTree()
           
 java.lang.String getTraitName()
          Returns the name of the trait cluster for this result.
 double[] getUSD(EMResult best, int kmin, int kmax, java.lang.String criterion)
           
 void setClusterings(EMResult[] results)
           
 void setClusterings(java.util.List list)
           
 void setQtlIdx(int[] qtlIdx)
          Set the indices of the Qtl which are implied in this result.
 void setSD(java.lang.Double[] sd)
          Set the standard deviations of the Qtl.
 void setTree(Tree tree)
           
 void setX(java.lang.Double[] xx)
          Set the observed positions of the Qtl.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

trait

public java.lang.String trait
The name of the trait.


nqtl

public int nqtl
The number of QTL


nmqc

public int nmqc
The number of meta qtl clusterings.


qtlIdx

public int[] qtlIdx
The indices of QTL which are implied in the analysis.


x

public double[] x
The QTL positions.


sd

public double[] sd
The QTL position standard deviations.


clusterings

public EMResult[] clusterings
The meta qtl clusterings.


tree

public Tree tree
The qtl tree

Constructor Detail

MetaQtlResult

public MetaQtlResult()

MetaQtlResult

public MetaQtlResult(java.lang.String trait,
                     int qtlNumber)
Parameters:
qtlNumber -
Method Detail

getClustering

public EMResult getClustering(int k)
Returns the Qtl clustering result with k clusters.

Parameters:
k -
Returns:

setClusterings

public void setClusterings(java.util.List list)
Parameters:
emResultList -

setClusterings

public void setClusterings(EMResult[] results)
Parameters:
emResults -

setQtlIdx

public void setQtlIdx(int[] qtlIdx)
Set the indices of the Qtl which are implied in this result.

Parameters:
qtlIdx - the indices of the Qtl.

setX

public void setX(java.lang.Double[] xx)
Set the observed positions of the Qtl.

Parameters:
xx -

setSD

public void setSD(java.lang.Double[] sd)
Set the standard deviations of the Qtl.

Parameters:
xx -

setTree

public void setTree(Tree tree)
Parameters:
tree -

getBestClustering

public EMResult getBestClustering(int criterion)
This methods returns the best models for each criterion defined to select the optimal number of clusters per trait.

Returns:

getTraitName

public java.lang.String getTraitName()
Returns the name of the trait cluster for this result.

Returns:
the name of the trait cluster.

getKValues

public int[] getKValues()
Returns:

getCriteria

public java.util.Iterator getCriteria()
Returns:

getCritValues

public double[] getCritValues(java.lang.String criterion,
                              int[] K)
Parameters:
criterion -
Returns:

getCritDelta

public double[] getCritDelta(java.lang.String criterion,
                             int[] K)
Parameters:
criterion -
Returns:

getCritWeights

public double[] getCritWeights(java.lang.String criterion,
                               int[] K)
Parameters:
criterion -
Returns:

getUSD

public double[] getUSD(EMResult best,
                       int kmin,
                       int kmax,
                       java.lang.String criterion)
Parameters:
best -
Returns:

getQtlTree

public Tree getQtlTree()
Returns:

getMetaQtl

public Qtl[] getMetaQtl(int k)
Returns: