SeqVarTools-package	SeqVarTools-package
allele-methods	allele-methods
alleleCount	alleleFrequency
alleleCount,SeqVarData-method	alleleFrequency
alleleCount,SeqVarGDSClass-method	alleleFrequency
alleleDosage	getGenotype
alleleDosage,SeqVarGDSClass,list-method	getGenotype
alleleDosage,SeqVarGDSClass,numeric-method	getGenotype
alleleFrequency	alleleFrequency
alleleFrequency,SeqVarData-method	alleleFrequency
alleleFrequency,SeqVarGDSClass-method	alleleFrequency
altChar	allele-methods
altChar,SeqVarGDSClass-method	allele-methods
altDosage	getGenotype
altDosage,SeqVarGDSClass-method	getGenotype
alternateAlleleDetection	alternateAlleleDetection
alternateAlleleDetection,SeqVarData,SeqVarData-method	alternateAlleleDetection
applyMethod	applyMethod
applyMethod,SeqVarGDSClass,function,character-method	applyMethod
applyMethod,SeqVarGDSClass,function,GRanges-method	applyMethod
applyMethod,SeqVarGDSClass,function,missing-method	applyMethod
applyMethod,SeqVarGDSClass,function,numeric-method	applyMethod
chromWithPAR	chromWithPAR
chromWithPAR,SeqVarGDSClass-method	chromWithPAR
countSingletons	countSingletons
countSingletons,SeqVarGDSClass-method	countSingletons
currentRanges	Iterator-class
currentRanges,SeqVarBlockIterator-method	Iterator-class
currentRanges,SeqVarListIterator-method	Iterator-class
currentRanges,SeqVarRangeIterator-method	Iterator-class
currentVariants	Iterator-class
currentVariants,SeqVarBlockIterator-method	Iterator-class
currentVariants,SeqVarIterator-method	Iterator-class
duplicateDiscordance	duplicateDiscordance
duplicateDiscordance,SeqVarData,missing-method	duplicateDiscordance
duplicateDiscordance,SeqVarData,SeqVarData-method	duplicateDiscordance
duplicateDiscordance,SeqVarIterator,missing-method	duplicateDiscordance
expandedAltDosage	getGenotype
expandedAltDosage,SeqVarGDSClass-method	getGenotype
expandedVariantIndex	variantInfo
expandedVariantIndex,SeqVarGDSClass-method	variantInfo
getGenotype	getGenotype
getGenotype,SeqVarGDSClass-method	getGenotype
getGenotypeAlleles	getGenotype
getGenotypeAlleles,SeqVarGDSClass-method	getGenotype
getVariableLengthData	getVariableLengthData
getVariableLengthData,SeqVarGDSClass,character-method	getVariableLengthData
granges	SeqVarData-class
granges,SeqVarData-method	SeqVarData-class
heterozygosity	heterozygosity
heterozygosity,SeqVarGDSClass-method	heterozygosity
hethom	heterozygosity
hethom,SeqVarGDSClass-method	heterozygosity
homozygosity	heterozygosity
homozygosity,SeqVarGDSClass-method	heterozygosity
hwe	hwe
hwe,SeqVarGDSClass-method	hwe
imputedDosage	imputedDosage
imputedDosage,SeqVarGDSClass-method	imputedDosage
inbreedCoeff	inbreedCoeff
inbreedCoeff,SeqVarGDSClass-method	inbreedCoeff
isSNV	isSNV
isSNV,SeqVarGDSClass-method	isSNV
isVariant	isVariant
isVariant,SeqVarGDSClass-method	isVariant
iterateFilter	Iterator-class
iterateFilter,SeqVarIterator-method	Iterator-class
lastFilter	Iterator-class
lastFilter,SeqVarIterator-method	Iterator-class
lastFilter<-	Iterator-class
lastFilter<-,SeqVarIterator,numeric-method	Iterator-class
meanBySample	meanBySample
meanBySample,SeqVarGDSClass-method	meanBySample
mendelErr	mendelErr
mendelErr,SeqVarGDSClass-method	mendelErr
minorAlleleCount	alleleFrequency
minorAlleleCount,SeqVarData-method	alleleFrequency
minorAlleleCount,SeqVarGDSClass-method	alleleFrequency
missingGenotypeRate	missingGenotypeRate
missingGenotypeRate,SeqVarGDSClass-method	missingGenotypeRate
nAlleles	allele-methods
nAlleles,SeqVarGDSClass-method	allele-methods
pca	pca
pca,SeqVarGDSClass-method	pca
pedigree	pedigree
refChar	allele-methods
refChar,SeqVarGDSClass-method	allele-methods
refDosage	getGenotype
refDosage,SeqVarGDSClass-method	getGenotype
refFrac	refFrac
refFrac,SeqVarGDSClass-method	refFrac
refFracOverHets	refFrac
refFracOverHets,SeqVarGDSClass-method	refFrac
refFracPlot	refFrac
refFracPlot,SeqVarGDSClass-method	refFrac
regression	regression
regression,SeqVarData-method	regression
resetIterator	Iterator-class
resetIterator,SeqVarIterator-method	Iterator-class
sampleData	SeqVarData-class
sampleData,SeqVarData-method	SeqVarData-class
sampleData<-	SeqVarData-class
sampleData<-,SeqVarData,AnnotatedDataFrame-method	SeqVarData-class
SeqVarBlockIterator	Iterator-class
SeqVarBlockIterator-class	Iterator-class
SeqVarData	SeqVarData-class
SeqVarData-class	SeqVarData-class
SeqVarIterator	Iterator-class
SeqVarIterator-class	Iterator-class
SeqVarListIterator	Iterator-class
SeqVarListIterator-class	Iterator-class
SeqVarRangeIterator	Iterator-class
SeqVarRangeIterator-class	Iterator-class
SeqVarTools	SeqVarTools-package
SeqVarWindowIterator	Iterator-class
SeqVarWindowIterator-class	Iterator-class
setVariantID	setVariantID
show,SeqVarData-method	SeqVarData-class
show,SeqVarIterator-method	Iterator-class
show,SeqVarListIterator-method	Iterator-class
show,SeqVarRangeIterator-method	Iterator-class
titv	titv
titv,SeqVarGDSClass-method	titv
validateSex	SeqVarData-class
validateSex,SeqVarData-method	SeqVarData-class
variantBlock	Iterator-class
variantBlock,SeqVarBlockIterator-method	Iterator-class
variantData	SeqVarData-class
variantData,SeqVarData-method	SeqVarData-class
variantData<-	SeqVarData-class
variantData<-,SeqVarData,AnnotatedDataFrame-method	SeqVarData-class
variantFilter	Iterator-class
variantFilter,SeqVarIterator-method	Iterator-class
variantInfo	variantInfo
variantInfo,SeqVarGDSClass-method	variantInfo
variantRanges	Iterator-class
variantRanges,SeqVarListIterator-method	Iterator-class
variantRanges,SeqVarRangeIterator-method	Iterator-class
