AffyExonPDInfo-class	DBPDInfo-class
AffyExpressionPDInfo-class	DBPDInfo-class
AffyGenePDInfo-class	DBPDInfo-class
affyPlatforms	affyPlatforms
AffySNPCNVPDInfo-class	DBPDInfo-class
AffySNPPDInfo-class	DBPDInfo-class
AffySTPDInfo-class	DBPDInfo-class
AffyTilingPDInfo-class	DBPDInfo-class
antisenseThetaA	snprmaSummaries
antisenseThetaA,SnpQSet-method	snprmaSummaries
antisenseThetaB	snprmaSummaries
antisenseThetaB,SnpQSet-method	snprmaSummaries
bgindex	Index-methods
bgindex,DBPDInfo-method	Index-methods
bgindex,FeatureSet-method	Index-methods
bgSequence	Sequences-methods
bgSequence,DBPDInfo-method	Sequences-methods
bgSequence,FeatureSet-method	Sequences-methods
calls	SnpCallSet-methods
calls,oligoSnpSet-method	oligoSnpSet-methods
calls,SnpCallSet-method	SnpCallSet-methods
calls,SnpLevelSet-method	SnpLevelSet-class
calls<-	SnpCallSet-methods
calls<-,oligoSnpSet,matrix-method	oligoSnpSet-methods
calls<-,SnpCallSet,matrix-method	SnpCallSet-methods
calls<-,SnpLevelSet,matrix-method	SnpLevelSet-class
callsConfidence	SnpCallSet-methods
callsConfidence,oligoSnpSet-method	oligoSnpSet-methods
callsConfidence,SnpCallSet-method	SnpCallSet-methods
callsConfidence,SnpLevelSet-method	SnpLevelSet-class
callsConfidence<-	SnpCallSet-methods
callsConfidence<-,oligoSnpSet,matrix-method	oligoSnpSet-methods
callsConfidence<-,SnpCallSet,matrix-method	SnpCallSet-methods
callsConfidence<-,SnpLevelSet,matrix-method	SnpLevelSet-class
chromosome	chromosome
chromosome,SnpLevelSet-method	SnpLevelSet-class
chromosome<-	chromosome
chromosome<-,AnnotatedDataFrame,character-method	chromosome
chromosome<-,SnpLevelSet,character-method	SnpLevelSet-class
cnConfidence	SnpCopyNumberSet-methods
cnConfidence,oligoSnpSet-method	oligoSnpSet-methods
cnConfidence,SnpCopyNumberSet-method	SnpCopyNumberSet-methods
cnConfidence,SnpLevelSet-method	SnpLevelSet-class
cnConfidence<-	SnpCopyNumberSet-methods
cnConfidence<-,oligoSnpSet,matrix-method	oligoSnpSet-methods
cnConfidence<-,SnpCopyNumberSet,matrix-method	SnpCopyNumberSet-methods
cnConfidence<-,SnpLevelSet,matrix-method	SnpLevelSet-class
coerce,SnpCallSetPlus,oligoSnpSet-method	SnpCallSetPlus-class
combine,SnpLevelSet,SnpLevelSet-method	SnpLevelSet-class
copyNumber	SnpCopyNumberSet-methods
copyNumber,oligoSnpSet-method	oligoSnpSet-methods
copyNumber,SnpCopyNumberSet-method	SnpCopyNumberSet-methods
copyNumber,SnpLevelSet-method	SnpLevelSet-class
copyNumber<-	SnpCopyNumberSet-methods
copyNumber<-,oligoSnpSet,matrix-method	oligoSnpSet-methods
copyNumber<-,SnpCopyNumberSet,matrix-method	SnpCopyNumberSet-methods
copyNumber<-,SnpLevelSet,matrix-method	SnpLevelSet-class
db	db
db,DBPDInfo-method	db
db,FeatureSet-method	db
db,SnpCallSet-method	db
db,SnpCallSetPlus-method	SnpCallSetPlus-class
db,SnpCnvQSet-method	db
db,SnpLevelSet-method	SnpLevelSet-class
db,SnpQSet-method	db
db-methods	db
DBPDInfo-class	DBPDInfo-class
efsExample	data-efsExample
ExonFeatureSet-class	FeatureSetExtensions-class
ExpressionFeatureSet-class	FeatureSetExtensions-class
ExpressionPDInfo-class	DBPDInfo-class
exprs,FeatureSet-method	exprs-methods
exprs-methods	exprs-methods
FeatureSet-class	FeatureSetExtensions-class
GeneFeatureSet-class	FeatureSetExtensions-class
genomeBuild	genomeBuild
genomeBuild,DBPDInfo-method	genomeBuild
genomeBuild,FeatureSet-method	genomeBuild
geometry	PDInfo-methods
geometry,DBPDInfo-method	PDInfo-methods
getA	SnpQSet-methods
getA,SnpCnvQSet-method	SnpQSet-methods
getA,SnpQSet-method	SnpQSet-methods
getA,TilingFeatureSet2-method	SnpQSet-methods
getM	SnpQSet-methods
getM,SnpCnvQSet-method	SnpQSet-methods
getM,SnpQSet-method	SnpQSet-methods
getM,TilingFeatureSet2-method	SnpQSet-methods
getPD	getPlatformDesign
getPlatformDesign	getPlatformDesign
getPlatformDesign,FeatureSet-method	getPlatformDesign
initialize,DBPDInfo-method	DBPDInfo-class
initialize,FeatureSet-method	FeatureSetExtensions-class
initialize,oligoSnpSet-method	oligoSnpSet-methods
initialize,SnpCallSet-method	SnpSetExtensions-class
initialize,SnpCallSetPlus-method	SnpCallSetPlus-class
initialize,SnpCnvCallSetPlus-method	SnpCallSetPlus-class
initialize,SnpCopyNumberSet-method	SnpSetExtensions-class
initialize,SnpQSet-method	SnpQSet-class
kind	kind
kind,AffyExonPDInfo-method	kind
kind,AffyExpressionPDInfo-method	kind
kind,AffyGenePDInfo-method	kind
kind,AffySNPCNVPDInfo-method	kind
kind,AffySNPPDInfo-method	kind
kind,ExpressionPDInfo-method	kind
kind,FeatureSet-method	kind
kind,TilingPDInfo-method	kind
length,FeatureSet-method	length-methods
length-methods	length-methods
manufacturer	manufacturer-methods
manufacturer,DBPDInfo-method	manufacturer-methods
manufacturer,FeatureSet-method	manufacturer-methods
manufacturer-methods	manufacturer-methods
mmindex	Index-methods
mmindex,DBPDInfo-method	Index-methods
mmindex,FeatureSet-method	Index-methods
mmSequence	Sequences-methods
mmSequence,AffySNPPDInfo-method	Sequences-methods
mmSequence,DBPDInfo-method	Sequences-methods
mmSequence,FeatureSet-method	Sequences-methods
NgsExpressionPDInfo-class	DBPDInfo-class
NgsTilingPDInfo-class	DBPDInfo-class
oligoSnpSet-class	oligoSnpSet-methods
pdPkgFromBioC	pdPkgFromBioC
platform	platform-methods
platform,FeatureSet-method	platform-methods
platform-methods	platform-methods
pmAllele	pmAllele
pmAllele,AffySNPPDInfo-method	pmAllele
pmAllele,SnpFeatureSet-method	pmAllele
pmChr	chromosome
pmChr,FeatureSet-method	chromosome
pmFragmentLength	pmFragmentLength-methods
pmFragmentLength,AffySNPPDInfo-method	pmFragmentLength-methods
pmFragmentLength-methods	pmFragmentLength-methods
pmindex	Index-methods
pmindex,DBPDInfo-method	Index-methods
pmindex,FeatureSet-method	Index-methods
pmOffset	pmPosition
pmOffset,AffySNPPDInfo-method	pmPosition
pmPosition	pmPosition
pmPosition,ExpressionPDInfo-method	pmPosition
pmPosition,TilingFeatureSet-method	pmPosition
pmPosition,TilingPDInfo-method	pmPosition
pmSequence	Sequences-methods
pmSequence,AffySNPPDInfo-method	Sequences-methods
pmSequence,DBPDInfo-method	Sequences-methods
pmSequence,FeatureSet-method	Sequences-methods
pmStrand	pmStrand
pmStrand,AffySNPPDInfo-method	pmStrand
position	position
position,SnpLevelSet-method	SnpLevelSet-class
probeNames	probeNames
probeNames,DBPDInfo-method	probeNames
probeNames,FeatureSet-method	probeNames
QuantificationSet-class	QuantificationSet-class
requireAnnotation	requireAnnotation
sampleNames,FeatureSet-method	sampleNames-methods
sampleNames-methods	sampleNames-methods
scqsExample	data-scqsExample
se.exprs,FeatureSet-method	exprs-methods
senseThetaA	snprmaSummaries
senseThetaA,SnpQSet-method	snprmaSummaries
senseThetaB	snprmaSummaries
senseThetaB,SnpQSet-method	snprmaSummaries
sfsExample	data-sfsExample
show,DBPDInfo-method	DBPDInfo-class
show,FeatureSet-method	FeatureSetExtensions-class
SnpCallSet-class	SnpSetExtensions-class
SnpCallSet-methods	SnpSetExtensions-class
SnpCallSetPlus-class	SnpCallSetPlus-class
SnpCnvCallSetPlus-class	SnpCallSetPlus-class
SnpCnvFeatureSet-class	FeatureSetExtensions-class
SNPCNVPDInfo-class	DBPDInfo-class
SnpCnvQSet-class	SnpCnvQSet-class
SnpCopyNumberSet-class	SnpSetExtensions-class
SnpCopyNumberSet-methods	SnpSetExtensions-class
SnpFeatureSet-class	FeatureSetExtensions-class
SnpLevelSet-class	SnpLevelSet-class
SNPPDInfo-class	DBPDInfo-class
SnpQSet-class	SnpQSet-class
sqsExample	data-sqsExample
thetaA	snprmaSummaries
thetaA,SnpCnvQSet-method	snprmaSummaries
thetaB	snprmaSummaries
thetaB,SnpCnvQSet-method	snprmaSummaries
TilingFeatureSet-class	FeatureSetExtensions-class
TilingPDInfo-class	DBPDInfo-class
