umcg.genetica.gwas

Class Dependifier

java.lang.Object

umcg.genetica.gwas.Dependifier

public class Dependifier
extends Object

Author:

harm-jan

Constructor Summary

Constructors

Constructor and Description
Dependifier(String datadir)
Dependifier(TriTyperGenotypeData dataset, SNPLoader loader)

Method Summary

Modifier and Type	Method and Description
HashSet<String>	dependify(String[] inputsnps, double proxyldthreshold, int maxproxydistance)
HashSet<String>	dependify(String[] needles, String[] haystack, double proxyldthreshold, int maxproxydistance)
HashMap<String,HashSet<String>>	dependifyReturnProxiesPerSNP(String[] inputsnps, double proxyldthreshold, int maxproxydistance)
HashMap<String,HashSet<String>>	dependifyReturnProxiesPerSNP(String[] needles, String[] haystack, double proxyldthreshold, int maxproxydistance)
HashSet<String>	findProxiesForSNP(String snp, double proxyldthreshold, int maxproxydistance)

Methods inherited from class java.lang.Object

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

Constructor Detail

Dependifier

public Dependifier(String datadir)
            throws IOException

Throws:

IOException

Dependifier

public Dependifier(TriTyperGenotypeData dataset,
                   SNPLoader loader)

Method Detail

dependifyReturnProxiesPerSNP

public HashMap<String,HashSet<String>> dependifyReturnProxiesPerSNP(String[] inputsnps,
                                                                    double proxyldthreshold,
                                                                    int maxproxydistance)
                                                             throws IOException

Throws:

IOException

dependify

public HashSet<String> dependify(String[] inputsnps,
                                 double proxyldthreshold,
                                 int maxproxydistance)
                          throws IOException

Throws:

IOException

dependify

public HashSet<String> dependify(String[] needles,
                                 String[] haystack,
                                 double proxyldthreshold,
                                 int maxproxydistance)
                          throws IOException

Throws:

IOException

dependifyReturnProxiesPerSNP

public HashMap<String,HashSet<String>> dependifyReturnProxiesPerSNP(String[] needles,
                                                                    String[] haystack,
                                                                    double proxyldthreshold,
                                                                    int maxproxydistance)
                                                             throws IOException

Throws:

IOException

findProxiesForSNP

public HashSet<String> findProxiesForSNP(String snp,
                                         double proxyldthreshold,
                                         int maxproxydistance)
                                  throws IOException

Throws:

IOException