$,ParESet-method	ParESet-class
$<-,ParESet-method	ParESet-class
addFeatureData	addFeatureData-method
addFeatureData,eSet-method	addFeatureData-method
addFeatureData-methods	addFeatureData-method
alleleA	alleleA
alleleA,AnnotatedDataFrame-method	alleleA
alleleA,SnpLevelSet-method	alleleA
alleleB	alleleB
alleleB,AnnotatedDataFrame-method	alleleB
alleleB,SnpLevelSet-method	alleleB
allPlots	allPlots-methods
allPlots,ParESet-method	ParESet-class
AnnotatedSnpCallSet-class	DEPRECATED-classes
AnnotatedSnpCopyNumberSet-class	DEPRECATED-classes
AnnotatedSnpSet-class	DEPRECATED-classes
calculateCopyNumber	calculateCopyNumber
calculateCopyNumber,SnpQSet-method	calculateCopyNumber
calculateCopyNumber-methods	calculateCopyNumber
centromere	centromere
chromosome	chromosome
chromosome,AnnotatedDataFrame-method	chromosome
chromosome,SnpLevelSet-method	chromosome
chromosome-methods	chromosome
chromosomeAnnotation	chromosomeAnnotation
chromosomeSize	chromosomeSize
coerce,AnnotatedSnpCallSet,SnpCallSet-method	coerce-methods
coerce,AnnotatedSnpCopyNumberSet,SnpCopyNumberSet-method	coerce-methods
coerce,AnnotatedSnpSet,oligoSnpSet-method	coerce-methods
coerce-methods	coerce-methods
cytoband	cytoband
dbSnpId	dbSnpId
dbSnpId,AnnotatedDataFrame-method	dbSnpId
dbSnpId,SnpLevelSet-method	dbSnpId
enzyme	enzyme
enzyme,AnnotatedDataFrame-method	enzyme
enzyme,SnpLevelSet-method	enzyme
fragmentLength	fragmentLength
fragmentLength,AnnotatedDataFrame-method	fragmentLength
fragmentLength,SnpLevelSet-method	fragmentLength
getPar	getPar-methods
getPar,SnpLevelSet-method	getPar-methods
getPar-methods	getPar-methods
getSnpAnnotation	getSnpAnnotation
getSnpAnnotation,oligoSnpSet-method	getSnpAnnotation
getSnpAnnotation,SnpCallSet-method	getSnpAnnotation
getSnpAnnotation,SnpCopyNumberSet-method	getSnpAnnotation
getSnpAnnotation,SnpLevelSet-method	getSnpAnnotation
hapmap	hapmap
initialize,oligoSnpSet-method	initialize-methods
initialize,ParESet-method	ParESet-class
initialize,ParSnpCallSet-method	ParSnpCallSet-class
initialize,ParSnpCopyNumberSet-method	ParSnpCopyNumberSet-class
initialize,ParSnpSet-method	ParSnpSet-class
initialize-methods	initialize-methods
ParESet-class	ParESet-class
ParSnpCallSet-class	ParSnpCallSet-class
ParSnpCopyNumberSet-class	ParSnpCopyNumberSet-class
ParSnpSet-class	ParSnpSet-class
plotCytoband	plotCytoband
plotSnp	plotSnp
plotSnp,ParESet,ANY-method	plotSnp
plotSnp,ParSnpCallSet,SnpCallSet-method	plotSnp
plotSnp,ParSnpCopyNumberSet,SnpCopyNumberSet-method	plotSnp
plotSnp,ParSnpSet,oligoSnpSet-method	plotSnp
position	position
position,AnnotatedDataFrame-method	position
position,SnpLevelSet-method	position
sample.snpset	sample.snpset
selectSomeIndex	selectSomeIndex
selectSomeIndex,data.frame-method	selectSomeIndex
show,oligoSnpSet-method	show-methods
show-methods	show-methods
showSummary	showSummary
smoothSnp	smoothSnp
smoothSnp,oligoSnpSet-method	smoothSnp
snpPar	snpPar
snpPar,ParESet-method	ParESet-class
snpPar<-	snpPar
snpPar<-,ParESet-method	ParESet-class
summary,AnnotatedSnpSet-method	summary-methods
summary,ANY-method	summary-methods
summary,oligoSnpSet-method	summary-methods
summary,SnpCallSet-method	summary-methods
summary-methods	summary-methods
unsplitSnpSet	unsplitSnpSet
unsplitSnpSet,list,AnnotatedDataFrame-method	unsplitSnpSet
unsplitSnpSet-methods	unsplitSnpSet
updateObject,AnnotatedSnpSet-method	updateObject-methods
updateObject,oligoSnpSet-method	updateObject-methods
