pal.popgen
public class LinkageDisequilibrium extends java.lang.Thread implements java.io.Serializable, TableReport
Modifier and Type | Field and Description |
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protected Alignment |
theAlignment |
protected AnnotationAlignment |
theAnnotationAlignment |
Constructor and Description |
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LinkageDisequilibrium(Alignment alignment)
compute LD based on an alignment.
|
LinkageDisequilibrium(Alignment alignment,
boolean rapidPermute,
int numberOfPermutations)
compute LD based on an alignment
|
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
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java.lang.Object[] |
getTableColumnNames()
get the names of the columns
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java.lang.Object[][] |
getTableData()
get the data elements
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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
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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
protected Alignment theAlignment
protected AnnotationAlignment theAnnotationAlignment
public LinkageDisequilibrium(Alignment alignment)
alignment
- Alignment or AnnotationAlignment (this should only contain
polymorphic sites)public LinkageDisequilibrium(Alignment alignment, boolean rapidPermute, int numberOfPermutations)
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 valuespublic void run()
run
in interface java.lang.Runnable
run
in class java.lang.Thread
public double getP(int r, int c)
r
- is site 1c
- is site 2public int getN(int r, int c)
r
- is site 1c
- is site 2public double getDPrime(int r, int c)
r
- is site 1c
- is site 2public double getRSqr(int r, int c)
r
- is site 1c
- is site 2public int getSiteCount()
public AnnotationAlignment getAnnotatedAlignment()
public java.lang.String toString()
toString
in class java.lang.Thread
public void print(LinkageDisequilibrium ld, java.io.PrintWriter out)
public java.lang.Object[] getTableColumnNames()
TableReport
getTableColumnNames
in interface TableReport
public java.lang.Object[][] getTableData()
TableReport
getTableData
in interface TableReport
public java.lang.String getTableTitle()
TableReport
getTableTitle
in interface TableReport