umcg.genetica.gwas

Class Independifier

java.lang.Object

umcg.genetica.gwas.Independifier

public class Independifier
extends Object

All shall be independent.

Author:

juha

Constructor Summary

Constructors

Constructor and Description
Independifier(String datadir)
Independifier(TriTyperGenotypeData genotypeData, SNPLoader snpLoader)

Method Summary

Modifier and Type	Method and Description
void	addPermutationDataset(String name, String filename)
String[]	independify(String[] snps, double r2Threshold, int bpThreshold) Independifies given SNPs with given thresholds.
String[]	independify(String permutationDataset, int permutation, double pThreshold, double r2Threshold, int bpThreshold, int nrIndependentSNPsWanted)
String[]	independify(String permutationDataset, int permutation, double pThreshold, double r2Threshold, int bpThreshold, int nrIndependentSNPsWanted, String outFile)
void	selectSNPsWithSimilarMAFsAsRealInputSNPs(String[] snps)

Methods inherited from class java.lang.Object

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

Constructor Detail

Independifier

public Independifier(String datadir)
              throws IOException

Throws:

IOException

Independifier

public Independifier(TriTyperGenotypeData genotypeData,
                     SNPLoader snpLoader)
              throws IOException

Throws:

IOException

Method Detail

selectSNPsWithSimilarMAFsAsRealInputSNPs

public void selectSNPsWithSimilarMAFsAsRealInputSNPs(String[] snps)
                                              throws IOException

Throws:

IOException

independify

public String[] independify(String[] snps,
                            double r2Threshold,
                            int bpThreshold)
                     throws IOException

Independifies given SNPs with given thresholds.

Parameters:

snps -

r2Threshold -

bpThreshold - Base pair distance threshold, ld will be calculated for SNPs

Returns:

Throws:

IOException

independify

public String[] independify(String permutationDataset,
                            int permutation,
                            double pThreshold,
                            double r2Threshold,
                            int bpThreshold,
                            int nrIndependentSNPsWanted)
                     throws IOException

Throws:

IOException

addPermutationDataset

public void addPermutationDataset(String name,
                                  String filename)
                           throws IOException

Throws:

IOException

independify

public String[] independify(String permutationDataset,
                            int permutation,
                            double pThreshold,
                            double r2Threshold,
                            int bpThreshold,
                            int nrIndependentSNPsWanted,
                            String outFile)
                     throws IOException

Throws:

IOException