$,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
centromere	centromere
chromosome	featureData-accessors
chromosome,AnnotatedDataFrame-method	featureData-accessors
chromosome,oligoSnpSet-method	featureData-accessors
chromosome,SnpCallSet-method	featureData-accessors
chromosome,SnpCopyNumberSet-method	featureData-accessors
chromosome,SnpLevelSet-method	featureData-accessors
chromosome-methods	featureData-accessors
chromosome2numeric	chromosome2numeric
chromosomeAnnotation	chromosomeAnnotation
chromosomeSize	chromosomeSize
cnConfidence,RatioSnpSet-method	RatioSnpSet-methods
cnConfidence<-,RatioSnpSet,matrix-method	RatioSnpSet-methods
coerce,AnnotatedSnpCallSet,SnpCallSet-method	coerce-methods
coerce,AnnotatedSnpCopyNumberSet,SnpCopyNumberSet-method	coerce-methods
coerce,AnnotatedSnpSet,oligoSnpSet-method	coerce-methods
coerce,oligoSnpSet,SnpCallSet-method	coerce-methods
coerce,oligoSnpSet,SnpCopyNumberSet-method	coerce-methods
coerce-methods	coerce-methods
copyNumber,RatioSnpSet-method	RatioSnpSet-methods
copyNumber<-,RatioSnpSet,matrix-method	RatioSnpSet-methods
crlmmOut	crlmmOut
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
getPar,ParESet-method	getPar
hapmap	hapmap
hmmPredict	hmmPredict
hmmPredict,ParESet-method	ParESet-class
HmmPredict-class	HmmPredict-class
initialize,ParESet-method	ParESet-class
initialize,ParSnpCallSet-method	ParSnpCallSet-class
initialize,ParSnpCopyNumberSet-method	ParSnpCopyNumberSet-class
initialize,ParSnpSet-method	ParSnpSet-class
initialize,RatioSnpSet-method	RatioSnpSet-methods
ParESet-class	ParESet-class
ParSnpCallSet-class	ParSnpCallSet-class
ParSnpCopyNumberSet-class	ParSnpCopyNumberSet-class
ParSnpSet-class	ParSnpSet-class
plotCytoband	plotCytoband
plotPredictions	plotPredictions
plotSnp	plotSnp
plotSnp,ParESet,SnpLevelSet-method	ParESet-class
plotSnp,ParSnpCallSet,SnpCallSet-method	plotSnp
plotSnp,ParSnpCopyNumberSet,SnpCopyNumberSet-method	plotSnp
plotSnp,ParSnpSet,oligoSnpSet-method	plotSnp
plotSnp,SnpLevelSet-method	plotSnp
position	featureData-accessors
position,AnnotatedDataFrame-method	featureData-accessors
position,oligoSnpSet-method	featureData-accessors
position,SnpCallSet-method	featureData-accessors
position,SnpCopyNumberSet-method	featureData-accessors
position,SnpLevelSet-method	featureData-accessors
position-methods	featureData-accessors
ratio	RatioSnpSet-methods
ratio,RatioSnpSet-method	RatioSnpSet-methods
ratio,SnpLevelSet-method	RatioSnpSet-methods
ratio<-	RatioSnpSet-methods
ratio<-,SnpLevelSet,matrix-method	RatioSnpSet-methods
ratioConfidence	RatioSnpSet-methods
ratioConfidence,RatioSnpSet-method	RatioSnpSet-methods
ratioConfidence<-	RatioSnpSet-methods
ratioConfidence<-,RatioSnpSet,matrix-method	RatioSnpSet-methods
RatioSnpSet-class	RatioSnpSet-class
RatioSnpSet-methods	RatioSnpSet-methods
sample.snpset	sample.snpset
selectSomeIndex	selectSomeIndex
selectSomeIndex,data.frame-method	selectSomeIndex
show,oligoSnpSet-method	show-methods
show,ParESet-method	show-methods
show,ParSnpCallSet-method	show-methods
show,ParSnpCopyNumberSet-method	show-methods
show,ParSnpSet-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
snpset	snpset
snpset,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
updateObject,oligoSnpSet-method	updateObject-methods
