edu.mssm.crover.tools.mapstrength
Class mapstrength

java.lang.Object
  |
  +--edu.mssm.crover.tools.mapstrength.mapstrength

public class mapstrength

extends java.lang.Object

Evaluates if a gene picking experiments which maps genes to given loci is statistically significant. Assume one performs a micro-array experiment and picks n genes that map to p well defined loci of a genome. The question which mapstrength helps assess is what is the probability that the mapping can be obtained by chance.

Version:

$Revision: 1.2 $

Author:

Fabien Campagne

Constructor Summary

mapstrength()

Method Summary

void	addTargetLocus(java.lang.String locus)
void	clearTargetLoci() Clears the set of target loci.
int	evaluate() Evaluate the number of random matches to the target loci.
int	getPickNumber()
int	getRepeatNumber()
static void	main(java.lang.String[] args)
static void	message(java.lang.String msg)
boolean	readLocusLink(java.lang.String filename)
boolean	readTargetLoci(java.lang.String filename) Read a file with one locus per line.
MapStrengthStats	repeatEvaluate() Evaluate the number of random matches to the target loci.
void	setPickNumber(int pickNumber)
void	setRepeatNumber(int repeatNumber)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

mapstrength

public mapstrength()

Method Detail

main

public static void main(java.lang.String[] args)

getPickNumber

public int getPickNumber()

setPickNumber

public void setPickNumber(int pickNumber)

addTargetLocus

public void addTargetLocus(java.lang.String locus)
                    throws LocusSyntaxErrorException

LocusSyntaxErrorException

readTargetLoci

public boolean readTargetLoci(java.lang.String filename)
                       throws java.io.FileNotFoundException,
                              java.io.IOException

Read a file with one locus per line. Add each locus to the set of target loci.

java.io.FileNotFoundException

java.io.IOException

clearTargetLoci

public void clearTargetLoci()

Clears the set of target loci.

readLocusLink

public boolean readLocusLink(java.lang.String filename)
                      throws UnsupportedFormatException,
                             SyntaxErrorException,
                             java.io.FileNotFoundException

UnsupportedFormatException

SyntaxErrorException

java.io.FileNotFoundException

message

public static void message(java.lang.String msg)

evaluate

public int evaluate()

Evaluate the number of random matches to the target loci.

repeatEvaluate

public MapStrengthStats repeatEvaluate()

Evaluate the number of random matches to the target loci.

getRepeatNumber

public int getRepeatNumber()

setRepeatNumber

public void setRepeatNumber(int repeatNumber)