org.metaqtl.algo
Class QtlClustAlgorithm

java.lang.Object
  extended by org.metaqtl.algo.MetaAlgorithm
      extended by org.metaqtl.algo.ClustAlgorithm
          extended by org.metaqtl.algo.QtlClustAlgorithm
All Implemented Interfaces:
IMetaAlgorithm

public class QtlClustAlgorithm
extends ClustAlgorithm

This class defines methods to perform a QTL meta-analysis on a genetic map by applying a clustering of QTL based on a gaussian mixture model and the EM-algorihtm.


Field Summary
 
Fields inherited from class org.metaqtl.algo.ClustAlgorithm
chrName, chromosomes, missing_sd_mode, ontology, result, sd_mode
 
Fields inherited from class org.metaqtl.algo.MetaAlgorithm
logger, loggerUp, workAmount, workProgress
 
Constructor Summary
QtlClustAlgorithm(IBioGenome map, IBioOntology ontology)
           
QtlClustAlgorithm(IBioGenome map, java.lang.String chrom, IBioOntology ontology)
           
 
Method Summary
 MetaQtlResult[] doQtlClustering(MetaQtlData data)
          For a given data set data performs the clustering on each trait group and returns the results as an array of MetaQtlResult objects.
 double getEMEps()
           
 int getEMRanStartNumber()
           
 void run()
          This method performs a QTL meta-analysis on each chromosome of the given map.
 void setEMEps(double epsilon)
           
 void setEMRanStartNumber(int n)
           
 void setMaxClusterNumber(int nmax)
           
 
Methods inherited from class org.metaqtl.algo.ClustAlgorithm
getResult, setCIMiss, setCIMode
 
Methods inherited from class org.metaqtl.algo.MetaAlgorithm
disableLogger, getLogger, getWorkAmount, getWorkProgress, isLoggerEnable, setLogger, setLogger
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

QtlClustAlgorithm

public QtlClustAlgorithm(IBioGenome map,
                         IBioOntology ontology)
Parameters:
map -
ontology -

QtlClustAlgorithm

public QtlClustAlgorithm(IBioGenome map,
                         java.lang.String chrom,
                         IBioOntology ontology)
Method Detail

run

public void run()
This method performs a QTL meta-analysis on each chromosome of the given map. For each chromosome all the possible QTL cluster combinations are tested and the results are added to the chromosome. Then the method returns the array of chromosomes for which the meta-analysis has been performed.


doQtlClustering

public MetaQtlResult[] doQtlClustering(MetaQtlData data)
For a given data set data performs the clustering on each trait group and returns the results as an array of MetaQtlResult objects.

Parameters:
data - the data set.
Returns:
the results of teh clustering.
See Also:
MetaQtlData, MetaQtlResult

setMaxClusterNumber

public void setMaxClusterNumber(int nmax)
Parameters:
nmax - the maximum number of clusters to test.

getEMRanStartNumber

public int getEMRanStartNumber()
Returns:
Returns the number of random starting points.

setEMRanStartNumber

public void setEMRanStartNumber(int n)
Parameters:
n_em_start - The n_em_start to set.

getEMEps

public double getEMEps()
Returns:
Returns the convergence error for the EM.

setEMEps

public void setEMEps(double epsilon)
Parameters:
em_err - The em_err to set.