LinkageDisequilibrium

java.lang.Object
- java.lang.Thread
- - pal.popgen.LinkageDisequilibrium

All Implemented Interfaces:

java.io.Serializable, java.lang.Runnable, TableReport
```
public class LinkageDisequilibrium
extends java.lang.Thread
implements java.io.Serializable, TableReport
```
This class calculates D' and r^2 estimates of linkage disequilibrium. It also calculates the significance of the LD by either Fisher Exact or the multinomial permutation test. This class can work with either normal alignments of annotated alignments. The alignments should be stripped of invariable sites. 2 state estimates of D' and r^2 can be found reviewed and discussed in Weir 1996 multi-state loci (>=3) require an averaging approach. These should not be used for popgen parameter estimates, unless you know specifically that it works for multistate loci. The estimate of D' is the approach used by Farnir 2000 Genome Research 10:220-227 that follows Hedrick 1987. r^2 was estimated in a similar way.

Version:

$Id: LinkageDisequilibrium.java,v 1

Author:

Ed Buckler

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class java.lang.Thread
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type Field and Description

protected Alignment theAlignment

protected AnnotationAlignment theAnnotationAlignment
- Fields inherited from class java.lang.Thread
  MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Fields
Modifier and Type	Field and Description
`protected Alignment`	`theAlignment`
`protected AnnotationAlignment`	`theAnnotationAlignment`

Constructor Summary

Constructors
Constructor and Description
`LinkageDisequilibrium(Alignment alignment)` compute LD based on an alignment.
`LinkageDisequilibrium(Alignment alignment, boolean rapidPermute, int numberOfPermutations)` compute LD based on an alignment

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`AnnotationAlignment`	`getAnnotatedAlignment()` Returns an annotated aligment if one was used for this LD this could be used to access information of locus position
`double`	`getDPrime(int r, int c)` Returns D' estimate for a given pair of sites
`int`	`getN(int r, int c)` Get number of gametes included in LD calculations (after missing data was excluded)
`double`	`getP(int r, int c)` Returns P-value estimate for a given pair of sites.
`double`	`getRSqr(int r, int c)` Returns r^2 estimate for a given pair of sites
`int`	`getSiteCount()` Returns the counts of the sites in the alignment
`java.lang.Object[]`	`getTableColumnNames()` get the names of the columns
`java.lang.Object[][]`	`getTableData()` get the data elements
`java.lang.String`	`getTableTitle()` get the title of the table
`void`	`print(LinkageDisequilibrium ld, java.io.PrintWriter out)` print the LD to the PrintWrite
`void`	`run()` starts the thread to calculate LD
`java.lang.String`	`toString()` returns representation of the LD results as a string

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, yield

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - theAlignment
```
protected Alignment theAlignment
```
  - theAnnotationAlignment
```
protected AnnotationAlignment theAnnotationAlignment
```
- Constructor Detail
  - LinkageDisequilibrium
```
public LinkageDisequilibrium(Alignment alignment)
```
    compute LD based on an alignment. The default is to used used rapid permutations that provides slightly biased P-values, and 1000 permutations to evaluate P-values.
    
    Parameters:
    
    alignment - Alignment or AnnotationAlignment (this should only contain polymorphic sites)
  - LinkageDisequilibrium
```
public LinkageDisequilibrium(Alignment alignment,
                             boolean rapidPermute,
                             int numberOfPermutations)
```
    compute LD based on an alignment
    
    Parameters:
    
    alignment - Alignment or AnnotationAlignment (this should only contain polymorphic sites)
    
    rapidPermute - Use a rapid approach to P-value estimation (see Contigency Table)
    
    numberOfPermutations - The number of permutations to determine P values
- Method Detail
  - run
```
public void run()
```
    starts the thread to calculate LD
    
    Specified by:
    
    run in interface java.lang.Runnable
    
    Overrides:
    
    run in class java.lang.Thread
  - getP
```
public double getP(int r,
                   int c)
```
    Returns P-value estimate for a given pair of sites. If there were only 2 alleles at each locus, then the Fisher Exact P-value (one-tail) is returned. If more states then the permutaed Monte Carlo test is used.
    
    Parameters:
    
    r - is site 1
    
    c - is site 2
    
    Returns:
    
    P-value
  - getN
```
public int getN(int r,
                int c)
```
    Get number of gametes included in LD calculations (after missing data was excluded)
    
    Parameters:
    
    r - is site 1
    
    c - is site 2
    
    Returns:
    
    number of gametes
  - getDPrime
```
public double getDPrime(int r,
                        int c)
```
    Returns D' estimate for a given pair of sites
    
    Parameters:
    
    r - is site 1
    
    c - is site 2
    
    Returns:
    
    D'
  - getRSqr
```
public double getRSqr(int r,
                      int c)
```
    Returns r^2 estimate for a given pair of sites
    
    Parameters:
    
    r - is site 1
    
    c - is site 2
    
    Returns:
    
    D'
  - getSiteCount
```
public int getSiteCount()
```
    Returns the counts of the sites in the alignment
  - getAnnotatedAlignment
```
public AnnotationAlignment getAnnotatedAlignment()
```
    Returns an annotated aligment if one was used for this LD this could be used to access information of locus position
  - toString
```
public java.lang.String toString()
```
    returns representation of the LD results as a string
    
    Overrides:
    
    toString in class java.lang.Thread
  - print
```
public void print(LinkageDisequilibrium ld,
                  java.io.PrintWriter out)
```
    print the LD to the PrintWrite
  - getTableColumnNames
```
public java.lang.Object[] getTableColumnNames()
```
    Description copied from interface: TableReport
    
    get the names of the columns
    
    Specified by:
    
    getTableColumnNames in interface TableReport
    
    Returns:
    
    column names for the table
  - getTableData
```
public java.lang.Object[][] getTableData()
```
    Description copied from interface: TableReport
    
    get the data elements
    
    Specified by:
    
    getTableData in interface TableReport
    
    Returns:
    
    data for the table
  - getTableTitle
```
public java.lang.String getTableTitle()
```
    Description copied from interface: TableReport
    
    get the title of the table
    
    Specified by:
    
    getTableTitle in interface TableReport
    
    Returns:
    
    the title of the table

Class LinkageDisequilibrium

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

theAlignment

theAnnotationAlignment

Constructor Detail

LinkageDisequilibrium

LinkageDisequilibrium

Method Detail

run

getP

getN

getDPrime

getRSqr

getSiteCount

getAnnotatedAlignment

toString

print

getTableColumnNames

getTableData

getTableTitle