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)


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.