GWASTools-package	GWASTools-package
alleleFrequency	alleleFrequency
allequal	allequal
anomDetectBAF	anomDetectBAF
anomDetectLOH	anomDetectLOH
anomFilterBAF	anomDetectBAF
anomIdentifyLowQuality	anomIdentifyLowQuality
anomSegmentBAF	anomDetectBAF
anomSegStats	anomSegStats
anomStatsPlot	anomSegStats
apartSnpSelection	apartSnpSelection
asSnpMatrix	snpStats
assocTestCPH	assocTestCPH
assocTestFisherExact	assocTestFisherExact
assocTestRegression	assocTestRegression
autosomeCode	getVariable
autosomeCode,GdsGenotypeReader-method	GdsGenotypeReader-class
autosomeCode,GenotypeData-method	GenotypeData-class
autosomeCode,IntensityData-method	IntensityData-class
autosomeCode,MatrixGenotypeReader-method	MatrixGenotypeReader-class
autosomeCode,NcdfGenotypeReader-method	NcdfGenotypeReader-class
autosomeCode,NcdfIntensityReader-method	NcdfIntensityReader-class
autosomeCode,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
autosomeCode,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
BAFfromClusterMeans	BAFfromClusterMeans
BAFfromGenotypes	BAFfromGenotypes
batchChisqTest	batchTest
batchFisherTest	batchTest
centromeres	centromeres
centromeres.hg18	centromeres
centromeres.hg19	centromeres
checkNcdfGds	convertNcdfGds
chromIntensityPlot	chromIntensityPlot
close,GdsReader-method	GdsReader-class
close,GenotypeData-method	GenotypeData-class
close,IntensityData-method	IntensityData-class
close,NcdfReader-method	NcdfReader-class
close,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
close,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
convertGdsNcdf	convertNcdfGds
convertNcdfGds	convertNcdfGds
convertVcfGds	convertVcfGds
duplicateDiscordance	duplicateDiscordance
duplicateDiscordanceAcrossDatasets	duplicateDiscordanceAcrossDatasets
duplicateDiscordanceProbability	duplicateDiscordanceProbability
findBAFvariance	findBAFvariance
gdsCheckImputedDosage	gdsImputedDosage
GdsGenotypeReader	GdsGenotypeReader-class
GdsGenotypeReader-class	GdsGenotypeReader-class
gdsImputedDosage	gdsImputedDosage
GdsReader	GdsReader-class
GdsReader-class	GdsReader-class
gdsSetMissingGenotypes	ncdfSetMissingGenotypes
gdsSubset	gdsSubset
gdsSubsetCheck	gdsSubset
genoClusterPlot	genoClusterPlot
genoClusterPlotByBatch	genoClusterPlot
GenotypeData	GenotypeData-class
GenotypeData-class	GenotypeData-class
genotypeToCharacter	genotypeToCharacter
getAlleleA	getVariable
getAlleleA,GdsGenotypeReader-method	GdsGenotypeReader-class
getAlleleA,GenotypeData-method	GenotypeData-class
getAlleleA,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
getAlleleA,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
getAlleleB	getVariable
getAlleleB,GdsGenotypeReader-method	GdsGenotypeReader-class
getAlleleB,GenotypeData-method	GenotypeData-class
getAlleleB,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
getAlleleB,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
getAnnotation	getVariable
getAnnotation,ScanAnnotationDataFrame-method	ScanAnnotationDataFrame-class
getAnnotation,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
getAnnotation,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
getAnnotation,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
getAttribute	getVariable
getAttribute,GdsReader-method	GdsReader-class
getAttribute,NcdfReader-method	NcdfReader-class
getBAlleleFreq	getVariable
getBAlleleFreq,IntensityData-method	IntensityData-class
getBAlleleFreq,NcdfIntensityReader-method	NcdfIntensityReader-class
getChromosome	getVariable
getChromosome,GdsGenotypeReader-method	GdsGenotypeReader-class
getChromosome,GenotypeData-method	GenotypeData-class
getChromosome,IntensityData-method	IntensityData-class
getChromosome,MatrixGenotypeReader-method	MatrixGenotypeReader-class
getChromosome,NcdfGenotypeReader-method	NcdfGenotypeReader-class
getChromosome,NcdfIntensityReader-method	NcdfIntensityReader-class
getChromosome,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
getChromosome,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
getDimension	getVariable
getDimension,GdsReader-method	GdsReader-class
getDimension,NcdfReader-method	NcdfReader-class
getDimensionNames	NcdfReader-class
getDimensionNames,NcdfReader-method	NcdfReader-class
getGenotype	getVariable
getGenotype,GdsGenotypeReader-method	GdsGenotypeReader-class
getGenotype,GenotypeData-method	GenotypeData-class
getGenotype,MatrixGenotypeReader-method	MatrixGenotypeReader-class
getGenotype,NcdfGenotypeReader-method	NcdfGenotypeReader-class
getLogRRatio	getVariable
getLogRRatio,IntensityData-method	IntensityData-class
getLogRRatio,NcdfIntensityReader-method	NcdfIntensityReader-class
getMetadata	getVariable
getMetadata,ScanAnnotationDataFrame-method	ScanAnnotationDataFrame-class
getMetadata,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
getMetadata,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
getMetadata,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
getobj	getobj
getPosition	getVariable
getPosition,GdsGenotypeReader-method	GdsGenotypeReader-class
getPosition,GenotypeData-method	GenotypeData-class
getPosition,IntensityData-method	IntensityData-class
getPosition,MatrixGenotypeReader-method	MatrixGenotypeReader-class
getPosition,NcdfGenotypeReader-method	NcdfGenotypeReader-class
getPosition,NcdfIntensityReader-method	NcdfIntensityReader-class
getPosition,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
getPosition,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
getQuality	getVariable
getQuality,IntensityData-method	IntensityData-class
getQuality,NcdfIntensityReader-method	NcdfIntensityReader-class
getQuery	getVariable
getQuery,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
getQuery,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
getScanID	getVariable
getScanID,GdsGenotypeReader-method	GdsGenotypeReader-class
getScanID,GenotypeData-method	GenotypeData-class
getScanID,IntensityData-method	IntensityData-class
getScanID,MatrixGenotypeReader-method	MatrixGenotypeReader-class
getScanID,NcdfGenotypeReader-method	NcdfGenotypeReader-class
getScanID,NcdfIntensityReader-method	NcdfIntensityReader-class
getScanID,ScanAnnotationDataFrame-method	ScanAnnotationDataFrame-class
getScanID,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
getScanVariable	getVariable
getScanVariable,GenotypeData-method	GenotypeData-class
getScanVariable,IntensityData-method	IntensityData-class
getScanVariableNames	getVariable
getScanVariableNames,GenotypeData-method	GenotypeData-class
getScanVariableNames,IntensityData-method	IntensityData-class
getSex	getVariable
getSex,GenotypeData-method	GenotypeData-class
getSex,IntensityData-method	IntensityData-class
getSex,ScanAnnotationDataFrame-method	ScanAnnotationDataFrame-class
getSex,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
getSnpID	getVariable
getSnpID,GdsGenotypeReader-method	GdsGenotypeReader-class
getSnpID,GenotypeData-method	GenotypeData-class
getSnpID,IntensityData-method	IntensityData-class
getSnpID,MatrixGenotypeReader-method	MatrixGenotypeReader-class
getSnpID,NcdfGenotypeReader-method	NcdfGenotypeReader-class
getSnpID,NcdfIntensityReader-method	NcdfIntensityReader-class
getSnpID,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
getSnpID,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
getSnpVariable	getVariable
getSnpVariable,GenotypeData-method	GenotypeData-class
getSnpVariable,IntensityData-method	IntensityData-class
getSnpVariableNames	getVariable
getSnpVariableNames,GenotypeData-method	GenotypeData-class
getSnpVariableNames,IntensityData-method	IntensityData-class
getVariable	getVariable
getVariable,GdsGenotypeReader-method	GdsGenotypeReader-class
getVariable,GdsReader-method	GdsReader-class
getVariable,GenotypeData-method	GenotypeData-class
getVariable,IntensityData-method	IntensityData-class
getVariable,NcdfGenotypeReader-method	NcdfGenotypeReader-class
getVariable,NcdfIntensityReader-method	NcdfIntensityReader-class
getVariable,NcdfReader-method	NcdfReader-class
getVariable,ScanAnnotationDataFrame-method	ScanAnnotationDataFrame-class
getVariable,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
getVariable,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
getVariable,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
getVariableNames	getVariable
getVariableNames,GdsReader-method	GdsReader-class
getVariableNames,NcdfReader-method	NcdfReader-class
getVariableNames,ScanAnnotationDataFrame-method	ScanAnnotationDataFrame-class
getVariableNames,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
getVariableNames,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
getVariableNames,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
getX	getVariable
getX,IntensityData-method	IntensityData-class
getX,NcdfIntensityReader-method	NcdfIntensityReader-class
getY	getVariable
getY,IntensityData-method	IntensityData-class
getY,NcdfIntensityReader-method	NcdfIntensityReader-class
gwasExactHW	gwasExactHW
GWASTools	GWASTools-package
GWASTools-defunct	defunct
hasBAlleleFreq	getVariable
hasBAlleleFreq,IntensityData-method	IntensityData-class
hasBAlleleFreq,NcdfIntensityReader-method	NcdfIntensityReader-class
hasCoordVariable	NcdfReader-class
hasCoordVariable,NcdfReader-method	NcdfReader-class
hasLogRRatio	getVariable
hasLogRRatio,IntensityData-method	IntensityData-class
hasLogRRatio,NcdfIntensityReader-method	NcdfIntensityReader-class
hasQuality	getVariable
hasQuality,IntensityData-method	IntensityData-class
hasQuality,NcdfIntensityReader-method	NcdfIntensityReader-class
hasScanAnnotation	getVariable
hasScanAnnotation,GenotypeData-method	GenotypeData-class
hasScanAnnotation,IntensityData-method	IntensityData-class
hasScanVariable	getVariable
hasScanVariable,GenotypeData-method	GenotypeData-class
hasScanVariable,IntensityData-method	IntensityData-class
hasSex	getVariable
hasSex,GenotypeData-method	GenotypeData-class
hasSex,IntensityData-method	IntensityData-class
hasSex,ScanAnnotationDataFrame-method	ScanAnnotationDataFrame-class
hasSex,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
hasSnpAnnotation	getVariable
hasSnpAnnotation,GenotypeData-method	GenotypeData-class
hasSnpAnnotation,IntensityData-method	IntensityData-class
hasSnpVariable	getVariable
hasSnpVariable,GenotypeData-method	GenotypeData-class
hasSnpVariable,IntensityData-method	IntensityData-class
hasVariable	getVariable
hasVariable,GdsReader-method	GdsReader-class
hasVariable,GenotypeData-method	GenotypeData-class
hasVariable,IntensityData-method	IntensityData-class
hasVariable,NcdfReader-method	NcdfReader-class
hasVariable,ScanAnnotationDataFrame-method	ScanAnnotationDataFrame-class
hasVariable,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
hasVariable,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
hasVariable,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
hasX	getVariable
hasX,IntensityData-method	IntensityData-class
hasX,NcdfIntensityReader-method	NcdfIntensityReader-class
hasY	getVariable
hasY,IntensityData-method	IntensityData-class
hasY,NcdfIntensityReader-method	NcdfIntensityReader-class
hetByScanChrom	hetByScanChrom
hetBySnpSex	hetBySnpSex
HLA	HLA
HLA.hg18	HLA
HLA.hg19	HLA
ibdAreasDraw	ibdPlot
ibdAssignRelatedness	ibdPlot
ibdAssignRelatednessKing	ibdPlot
ibdPlot	ibdPlot
IntensityData	IntensityData-class
IntensityData-class	IntensityData-class
intensityOutliersPlot	intensityOutliersPlot
manhattanPlot	manhattanPlot
MatrixGenotypeReader	MatrixGenotypeReader-class
MatrixGenotypeReader-class	MatrixGenotypeReader-class
MchromCode	getVariable
MchromCode,GdsGenotypeReader-method	GdsGenotypeReader-class
MchromCode,GenotypeData-method	GenotypeData-class
MchromCode,IntensityData-method	IntensityData-class
MchromCode,MatrixGenotypeReader-method	MatrixGenotypeReader-class
MchromCode,NcdfGenotypeReader-method	NcdfGenotypeReader-class
MchromCode,NcdfIntensityReader-method	NcdfIntensityReader-class
MchromCode,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
MchromCode,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
meanIntensityByScanChrom	meanIntensityByScanChrom
meanSdByChromWindow	findBAFvariance
medianSdOverAutosomes	findBAFvariance
mendelErr	mendelErr
mendelList	mendelList
mendelListAsDataFrame	mendelList
minorAlleleDetectionAccuracy	duplicateDiscordanceAcrossDatasets
missingGenotypeByScanChrom	missingGenotypeByScanChrom
missingGenotypeBySnpSex	missingGenotypeBySnpSex
ncdfAddData	ncdfAddData
ncdfAddIntensity	ncdfAddData
ncdfCheckGenotype	ncdfAddData
ncdfCheckIntensity	ncdfAddData
ncdfCreate	ncdfCreate
NcdfGenotypeReader	NcdfGenotypeReader-class
NcdfGenotypeReader-class	NcdfGenotypeReader-class
ncdfImputedDosage	ncdfImputedDosage
NcdfIntensityReader	NcdfIntensityReader-class
NcdfIntensityReader-class	NcdfIntensityReader-class
NcdfReader	NcdfReader-class
NcdfReader-class	NcdfReader-class
ncdfSetMissingGenotypes	ncdfSetMissingGenotypes
ncdfSubset	ncdfSubset
ncdfSubsetCheck	ncdfSubset
nscan	getVariable
nscan,GdsGenotypeReader-method	GdsGenotypeReader-class
nscan,GenotypeData-method	GenotypeData-class
nscan,IntensityData-method	IntensityData-class
nscan,MatrixGenotypeReader-method	MatrixGenotypeReader-class
nscan,NcdfGenotypeReader-method	NcdfGenotypeReader-class
nscan,NcdfIntensityReader-method	NcdfIntensityReader-class
nscan,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
nsnp	getVariable
nsnp,GdsGenotypeReader-method	GdsGenotypeReader-class
nsnp,GenotypeData-method	GenotypeData-class
nsnp,IntensityData-method	IntensityData-class
nsnp,MatrixGenotypeReader-method	MatrixGenotypeReader-class
nsnp,NcdfGenotypeReader-method	NcdfGenotypeReader-class
nsnp,NcdfIntensityReader-method	NcdfIntensityReader-class
nsnp,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
open,GdsReader-method	GdsReader-class
open,GenotypeData-method	GenotypeData-class
open,IntensityData-method	IntensityData-class
open,NcdfReader-method	NcdfReader-class
open,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
open,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
pcaSnpFilters	pcaSnpFilters
pcaSnpFilters.hg18	pcaSnpFilters
pcaSnpFilters.hg19	pcaSnpFilters
pedigreeCheck	pedigreeCheck
pedigreeDeleteDuplicates	pedigreeDeleteDuplicates
pedigreeMaxUnrelated	pedigreeMaxUnrelated
pedigreePairwiseRelatedness	pedigreePairwiseRelatedness
plinkCheck	plinkUtils
plinkToNcdf	plinkToNcdf
plinkWrite	plinkUtils
pseudoautoIntensityPlot	pseudoautoIntensityPlot
pseudoautosomal	pseudoautosomal
pseudoautosomal.hg18	pseudoautosomal
pseudoautosomal.hg19	pseudoautosomal
qqPlot	qqPlot
qualityScoreByScan	qualityScoreByScan
qualityScoreBySnp	qualityScoreBySnp
readWriteFirst	readWriteFirst
relationsMeanVar	relationsMeanVar
saveas	saveas
ScanAnnotationDataFrame	ScanAnnotationDataFrame-class
ScanAnnotationDataFrame-class	ScanAnnotationDataFrame-class
ScanAnnotationSQLite	ScanAnnotationSQLite-class
ScanAnnotationSQLite-class	ScanAnnotationSQLite-class
sdByScanChromWindow	findBAFvariance
show,GdsReader-method	GdsReader-class
show,GenotypeData-method	GenotypeData-class
show,IntensityData-method	IntensityData-class
show,MatrixGenotypeReader-method	MatrixGenotypeReader-class
show,NcdfReader-method	NcdfReader-class
show,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
show,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
simulateGenotypeMatrix	simulateGenotypeMatrix
simulateIntensityMatrix	simulateIntensityMatrix
SnpAnnotationDataFrame	SnpAnnotationDataFrame-class
SnpAnnotationDataFrame-class	SnpAnnotationDataFrame-class
SnpAnnotationSQLite	SnpAnnotationSQLite-class
SnpAnnotationSQLite-class	SnpAnnotationSQLite-class
snpCorrelationPlot	snpCorrelationPlot
writeAnnotation	getVariable
writeAnnotation,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
writeAnnotation,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
writeMetadata	getVariable
writeMetadata,ScanAnnotationSQLite-method	ScanAnnotationSQLite-class
writeMetadata,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
XchromCode	getVariable
XchromCode,GdsGenotypeReader-method	GdsGenotypeReader-class
XchromCode,GenotypeData-method	GenotypeData-class
XchromCode,IntensityData-method	IntensityData-class
XchromCode,MatrixGenotypeReader-method	MatrixGenotypeReader-class
XchromCode,NcdfGenotypeReader-method	NcdfGenotypeReader-class
XchromCode,NcdfIntensityReader-method	NcdfIntensityReader-class
XchromCode,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
XchromCode,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
XYchromCode	getVariable
XYchromCode,GdsGenotypeReader-method	GdsGenotypeReader-class
XYchromCode,GenotypeData-method	GenotypeData-class
XYchromCode,IntensityData-method	IntensityData-class
XYchromCode,MatrixGenotypeReader-method	MatrixGenotypeReader-class
XYchromCode,NcdfGenotypeReader-method	NcdfGenotypeReader-class
XYchromCode,NcdfIntensityReader-method	NcdfIntensityReader-class
XYchromCode,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
XYchromCode,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
YchromCode	getVariable
YchromCode,GdsGenotypeReader-method	GdsGenotypeReader-class
YchromCode,GenotypeData-method	GenotypeData-class
YchromCode,IntensityData-method	IntensityData-class
YchromCode,MatrixGenotypeReader-method	MatrixGenotypeReader-class
YchromCode,NcdfGenotypeReader-method	NcdfGenotypeReader-class
YchromCode,NcdfIntensityReader-method	NcdfIntensityReader-class
YchromCode,SnpAnnotationDataFrame-method	SnpAnnotationDataFrame-class
YchromCode,SnpAnnotationSQLite-method	SnpAnnotationSQLite-class
