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java.lang.Objectorg.metaqtl.Qtl
public class Qtl
A QTL (Quantitative Trait Loci)
Nested Class Summary | |
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class |
Qtl.QTLCross
This class stores the informations on the cross design used to detect the QTL. |
class |
Qtl.QTLProj
This class stores the QTL projection properties. |
class |
Qtl.QTLStats
This class stores the usual statistics for the QTL. |
class |
Qtl.QTLSupport
This class stores information on the QTL Confidence Interval |
class |
Qtl.QTLTrait
This class stores the trait description of a QTL |
Field Summary | |
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double |
c1
The recombination rate between the QTL position and the left flanking marker. |
double |
c2
The recombination rate between the QTL position and the right flanking marker. |
Qtl.QTLSupport |
ci
The QTL confidence interval. |
Qtl.QTLCross |
cross
The QTL cross design. |
int |
id
The id of the Qtl |
int |
m1
The indice of the left flanking marker. |
int |
m2
The indice of the right flanking marker. |
java.lang.String |
name
The name of the QTL. |
double |
position
The QTL most probable location on the chromosome. |
Qtl.QTLProj |
proj
The QTL projection properties. |
double |
sd_position
The standard deviation of the QTL position. |
Qtl.QTLStats |
stats
The QTL statistics |
Qtl.QTLTrait |
trait
The QTL trait data. |
Constructor Summary | |
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Qtl()
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Method Summary | |
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Qtl |
getCopy()
Returns a copy of the QTL. |
java.lang.String |
getName()
Returns the name of the QTL. |
static double |
getQTLSD(double rsquare,
Qtl.QTLCross cross,
int mappingUnit)
Depending on the r-square parameter and the cross design this method returns the standard deviation of the QTL position for the given mapping context. |
static double |
getQTLSD(Qtl.QTLSupport ci,
int mappingFunction,
int mappingUnit)
Depending on the CI type this methods returns the the standard deviation of the QTL position using the given mapping context. |
boolean |
isIgnore()
This methods returns true if the QTL must be ignored. |
void |
setIgnore(boolean ignore)
Set the status of the QTL. |
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 id
public java.lang.String name
public int m1
public int m2
public double position
public double sd_position
public double c1
public double c2
public Qtl.QTLTrait trait
public Qtl.QTLStats stats
public Qtl.QTLSupport ci
public Qtl.QTLCross cross
public Qtl.QTLProj proj
Constructor Detail |
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public Qtl()
Method Detail |
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public static double getQTLSD(Qtl.QTLSupport ci, int mappingFunction, int mappingUnit)
ci
- the confidence interval of the QTL.mappingFunction
- the mapping function.mappingUnit
- the mapping unit.
public static double getQTLSD(double rsquare, Qtl.QTLCross cross, int mappingUnit)
rsquare
-
public boolean isIgnore()
public void setIgnore(boolean ignore)
ignore
- the status of the QTL.public Qtl getCopy()
public java.lang.String getName()
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