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java.lang.Objectorg.metaqtl.MetaQtlAnalysis
public class MetaQtlAnalysis
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 | |
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MetaQtlAnalysis(int nchr)
Creates a new instance of a MetaQtlAnalysis |
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public int nchr
public java.lang.String[] chromNames
public Qtl[][] qtlByChrom
public MetaQtlResult[][] resultByChrom
Constructor Detail |
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public MetaQtlAnalysis(int nchr)
MetaQtlAnalysis
nchr
- the number of chromosomes on which the meta-analysis has been
performed.Method Detail |
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public MetaQtlResult getResult(java.lang.String chrom, java.lang.String trait)
trait
- the name of the trait for which the result is asked.
public MetaQtlResult getResult(java.lang.String chrom)
public MetaQtlResult getResult(int chromIdx, java.lang.String trait)
trait
- the name of the trait for which the result is asked.
public int getChromIdx(java.lang.String chrom)
public int getTraitIdx(int chromIdx, java.lang.String trait)
public Qtl[] getMetaQtl(java.lang.String chrom, java.lang.String trait, int k)
cidx
, the given trait name trait
and the given number of clusters k
.
cidx
- trait
- k
- public MetaQtlModel getBestModel(int criterion)
public MetaQtlResult[] getResults(java.lang.String chromName)
|
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