umcg.genetica.io.trityper

Class SNP

java.lang.Object

umcg.genetica.io.trityper.SNP

public class SNP
extends Object

Author:

harmjan

Field Summary

Fields

Modifier and Type	Field and Description
int	nrCalled

Constructor Summary

Constructors

Constructor and Description
SNP()

Method Summary

Modifier and Type	Method and Description
void	clearGenotypes()
byte[]	getAllele1()
byte[]	getAllele2()
double[]	getAlleleFreq()
byte	getAlleleItr()
byte[]	getAlleles()
byte	getChr()
int	getChrPos()
double	getCR()
double	getDosageMAF()
double[]	getDosageValues()
int[]	getGenotypeFreq()
byte[]	getGenotypes()
double	getHWEP()
int	getId()
double	getMAF()
byte	getMinorAllele()
String	getName()
int	getNrCalled()
boolean	hasDosageInformation()
boolean	passesQC()
double[]	selectGenotypes(int[] ids)
double[]	selectGenotypes(int[] phenotypeToGenotypeId, boolean includeMissingGenotypes, boolean loadDosageWhenAvailable)
double[]	selectGenotypes(short[] phenotypeToGenotypeId, boolean includeMissingGenotypes, boolean loadDosageWhenAvailable)
void	setAlleleCodes(byte[] alleles)
void	setAlleles(byte[] allele1, byte[] allele2)
void	setAlleles(byte[] allele1, byte[] allele2, Boolean[] indIncluded, Boolean[] indIsFemale)
void	setChr(byte chr)
void	setChrPos(int chrPos)
void	setCR(Double CR)
void	setDosage(byte[] dosageValues)
void	setGenotypeFreq(int[] genotypeFreq)
void	setHWEP(Double HWEP)
void	setId(int snpId)
void	setMAF(Double MAF)
void	setMinorAllele(byte minorAllele)
void	setName(String snp)
void	setNrCalled(int nrCalled)
void	setPassesQC(boolean b)

Methods inherited from class java.lang.Object

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

Field Detail

nrCalled

public int nrCalled

Constructor Detail

SNP

public SNP()

Method Detail

getAlleleItr

public byte getAlleleItr()

setChr

public void setChr(byte chr)

setChrPos

public void setChrPos(int chrPos)

getChr

public byte getChr()

getChrPos

public int getChrPos()

setId

public void setId(int snpId)

getId

public int getId()

setName

public void setName(String snp)

getName

public String getName()

setAlleles

public void setAlleles(byte[] allele1,
                       byte[] allele2,
                       Boolean[] indIncluded,
                       Boolean[] indIsFemale)

setPassesQC

public void setPassesQC(boolean b)

passesQC

public boolean passesQC()

getHWEP

public double getHWEP()

Returns:

the HWEP

setHWEP

public void setHWEP(Double HWEP)

Parameters:

HWEP - the HWEP to set

getMAF

public double getMAF()

Returns:

the MAF

getDosageMAF

public double getDosageMAF()

Returns:

the MAF calculated on the basis of dosage values

setMAF

public void setMAF(Double MAF)

Parameters:

MAF - the MAF to set

getCR

public double getCR()

Returns:

the CR

setCR

public void setCR(Double CR)

Parameters:

CR - the CR to set

setAlleles

public void setAlleles(byte[] allele1,
                       byte[] allele2)

clearGenotypes

public void clearGenotypes()

getAllele1

public byte[] getAllele1()

getAllele2

public byte[] getAllele2()

getGenotypes

public byte[] getGenotypes()

setDosage

public void setDosage(byte[] dosageValues)

getDosageValues

public double[] getDosageValues()

hasDosageInformation

public boolean hasDosageInformation()

selectGenotypes

public double[] selectGenotypes(int[] ids)

selectGenotypes

public double[] selectGenotypes(short[] phenotypeToGenotypeId,
                                boolean includeMissingGenotypes,
                                boolean loadDosageWhenAvailable)

selectGenotypes

public double[] selectGenotypes(int[] phenotypeToGenotypeId,
                                boolean includeMissingGenotypes,
                                boolean loadDosageWhenAvailable)

getAlleles

public byte[] getAlleles()

setAlleleCodes

public void setAlleleCodes(byte[] alleles)

getMinorAllele

public byte getMinorAllele()

getAlleleFreq

public double[] getAlleleFreq()

getGenotypeFreq

public int[] getGenotypeFreq()

Returns:

the genotypeFreq

setGenotypeFreq

public void setGenotypeFreq(int[] genotypeFreq)

Parameters:

genotypeFreq - the genotypeFreq to set

setMinorAllele

public void setMinorAllele(byte minorAllele)

setNrCalled

public void setNrCalled(int nrCalled)

getNrCalled

public int getNrCalled()