public class Independifier extends Object
| Constructor and Description |
|---|
Independifier(String datadir) |
Independifier(TriTyperGenotypeData genotypeData,
SNPLoader snpLoader) |
| 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) |
public Independifier(String datadir) throws IOException
IOExceptionpublic Independifier(TriTyperGenotypeData genotypeData, SNPLoader snpLoader) throws IOException
IOExceptionpublic void selectSNPsWithSimilarMAFsAsRealInputSNPs(String[] snps) throws IOException
IOExceptionpublic String[] independify(String[] snps, double r2Threshold, int bpThreshold) throws IOException
snps - r2Threshold - bpThreshold - Base pair distance threshold, ld will be calculated
for SNPsIOExceptionpublic String[] independify(String permutationDataset, int permutation, double pThreshold, double r2Threshold, int bpThreshold, int nrIndependentSNPsWanted) throws IOException
IOExceptionpublic void addPermutationDataset(String name, String filename) throws IOException
IOExceptionpublic String[] independify(String permutationDataset, int permutation, double pThreshold, double r2Threshold, int bpThreshold, int nrIndependentSNPsWanted, String outFile) throws IOException
IOExceptionCopyright © 2015. All Rights Reserved.