A	AlleleSet-methods
A,AlleleSet-method	AlleleSet-methods
A,CNSet-method	CNSet-class
A<-	AlleleSet-methods
A<-,AlleleSet,matrix-method	AlleleSet-methods
A<-,AlleleSet-method	AlleleSet-methods
A<-,CNSet-method	CNSet-class
AffyExonPDInfo	DBPDInfo-class
AffyExonPDInfo-class	DBPDInfo-class
AffyExpressionPDInfo	DBPDInfo-class
AffyExpressionPDInfo-class	DBPDInfo-class
AffyGenePDInfo	DBPDInfo-class
AffyGenePDInfo-class	DBPDInfo-class
affyPlatforms	affyPlatforms
AffySNPCNVPDInfo	DBPDInfo-class
AffySNPCNVPDInfo-class	DBPDInfo-class
AffySNPPDInfo	DBPDInfo-class
AffySNPPDInfo-class	DBPDInfo-class
AffySTPDInfo	DBPDInfo-class
AffySTPDInfo-class	DBPDInfo-class
AffyTilingPDInfo	DBPDInfo-class
AffyTilingPDInfo-class	DBPDInfo-class
allele	AlleleSet-class
allele,AlleleSet-method	AlleleSet-class
allele,CNSet-method	CNSet-class
allele,SnpFeatureSet-method	AlleleSet-class
AlleleSet	AlleleSet-class
AlleleSet-class	AlleleSet-class
annotatedDataFrameFrom,ff_matrix-method	ff_matrix
annotation,DBPDInfo-method	DBPDInfo-class
annotationPackages	annotationPackages
B	AlleleSet-methods
B,AlleleSet-method	AlleleSet-methods
B,CNSet-method	CNSet-class
B<-	AlleleSet-methods
B<-,AlleleSet,matrix-method	AlleleSet-methods
B<-,AlleleSet-method	AlleleSet-methods
B<-,CNSet-method	CNSet-class
baf	generics
baf,BeadStudioSet-method	BeadStudioSet-class
baf,oligoSnpSet-method	oligoSnpSet-methods
baf<-	BeadStudioSet-class
baf<-,BeadStudioSet-method	BeadStudioSet-class
baf<-,oligoSnpSet-method	oligoSnpSet-methods
batch	batch
batch,CNSet-method	CNSet-class
batchNames	batch
batchNames,AssayData-method	AssayData-methods
batchNames,CNSet-method	CNSet-class
batchNames<-	batch
batchNames<-,AssayData-method	AssayData-methods
batchNames<-,CNSet-method	CNSet-class
batchStatistics	batchStatistics
batchStatistics,CNSet-method	CNSet-class
batchStatistics<-	batchStatistics
batchStatistics<-,CNSet,AssayData-method	CNSet-class
BeadStudioSet	BeadStudioSet-class
BeadStudioSet-class	BeadStudioSet-class
bothStrands	AlleleSet-class
bothStrands,AlleleSet-method	AlleleSet-class
bothStrands,SnpFeatureSet-method	AlleleSet-class
calls	SnpSet-methods
calls,CNSet-method	CNSet-class
calls,oligoSnpSet-method	oligoSnpSet-methods
calls,SnpSet-method	SnpSet-methods
calls<-	SnpSet-methods
calls<-,CNSet,matrix-method	CNSet-class
calls<-,oligoSnpSet,matrix-method	oligoSnpSet-methods
calls<-,SnpSet,matrix-method	SnpSet-methods
callsConfidence,oligoSnpSet-method	oligoSnpSet-methods
callsConfidence<-,oligoSnpSet,matrix-method	oligoSnpSet-methods
celfileDate	celfileDate
checkExists	checkExists
checkOrder	checkOrder
checkOrder,CopyNumberSet-method	CopyNumberSet-class
checkOrder,gSet-method	gSet-class
checkOrder,SnpSet-method	SnpSet-methods
chromosome	chromosome-methods
chromosome,AnnotatedDataFrame-method	chromosome-methods
chromosome,GenomeAnnotatedDataFrame-method	chromosome-methods
chromosome,gSet-method	chromosome-methods
chromosome,RangedDataCNV-method	chromosome-methods
chromosome,SnpSet-method	chromosome-methods
chromosome-methods	chromosome-methods
chromosome2integer	chromosome2integer
chromosome<-	chromosome-methods
chromosome<-,GenomeAnnotatedDataFrame,integer-method	chromosome-methods
chromosome<-,gSet,integer-method	chromosome-methods
chromosome<-,SnpSet,integer-method	chromosome-methods
chromosomePositionOrder	checkOrder
close	fileConnections
close,AlleleSet-method	AlleleSet-methods
close,array-method	fileConnections
close,CNSet-method	CNSet-class
close,matrix-method	fileConnections
close,numeric-method	fileConnections
closeff	fileConnections
closeff,CNSet-method	fileConnections
cnConfidence	CopyNumberSet-methods
cnConfidence,CopyNumberSet-method	CopyNumberSet-class
cnConfidence,oligoSnpSet-method	oligoSnpSet-methods
cnConfidence<-	CopyNumberSet-methods
cnConfidence<-,CopyNumberSet,matrix-method	CopyNumberSet-class
cnConfidence<-,oligoSnpSet,matrix-method	oligoSnpSet-methods
CNSet	CNSet-class
CNSet-class	CNSet-class
coerce,AnnotatedDataFrame,GenomeAnnotatedDataFrame-method	GenomeAnnotatedDataFrame-class
coerce,BeadStudioSet,data.frame-method	BeadStudioSet-class
coerce,CNSet,CopyNumberSet-method	CNSet-class
coerce,CNSet,oligoSnpSet	CNSet-class
coerce,CNSet,oligoSnpSet-method	CNSet-class
coerce,CNSetLM,CNSet-method	CNSet-class
coerce,oligoSnpSet,data.frame-method	oligoSnpSet-methods
coerce,RangedData,RangedDataCBS-method	RangedDataCNV-classes
coerce,RangedData,RangedDataHMM-method	RangedDataCNV-classes
confs	SnpSet-methods
confs,CNSet-method	CNSet-class
confs,SnpSet-method	SnpSet-methods
confs<-	SnpSet-methods
confs<-,CNSet,matrix-method	CNSet-class
confs<-,SnpSet,matrix-method	SnpSet-methods
copyNumber	CopyNumberSet-methods
copyNumber,BeadStudioSet-method	BeadStudioSet-class
copyNumber,CopyNumberSet-method	CopyNumberSet-class
copyNumber,oligoSnpSet-method	oligoSnpSet-methods
copyNumber<-	CopyNumberSet-methods
copyNumber<-,BeadStudioSet,ANY-method	BeadStudioSet-class
copyNumber<-,CopyNumberSet,matrix-method	CopyNumberSet-class
copyNumber<-,oligoSnpSet,matrix-method	oligoSnpSet-methods
CopyNumberSet	CopyNumberSet-class
CopyNumberSet-class	CopyNumberSet-class
CopyNumberSet-methods	CopyNumberSet-methods
corr	AssayData-methods
corr,CNSet,character-method	CNSet-class
coverage2	RangedDataCNV-classes
coverage2,RangedDataCNV-method	RangedDataCNV-classes
createFF	createFF
db	db
db,AlleleSet-method	AlleleSet-class
db,DBPDInfo-method	db
db,FeatureSet-method	db
db,gSet-method	gSet-class
db,SnpCnvQSet-method	db
db,SnpQSet-method	db
db,SnpSet-method	db
db-methods	db
DBPDInfo	DBPDInfo-class
DBPDInfo-class	DBPDInfo-class
delCluster	clusterOptsDeprecated
delCluster-deprecated	clusterOptsDeprecated
efsExample	data-efsExample
ExonFeatureSet	FeatureSetExtensions-class
ExonFeatureSet-class	FeatureSetExtensions-class
ExpressionFeatureSet	FeatureSetExtensions-class
ExpressionFeatureSet-class	FeatureSetExtensions-class
ExpressionPDInfo	DBPDInfo-class
ExpressionPDInfo-class	DBPDInfo-class
exprs,FeatureSet-method	exprs-methods
exprs-methods	exprs-methods
FeatureSet	FeatureSetExtensions-class
FeatureSet-class	FeatureSetExtensions-class
featuresInRange	featuresInRange
featuresInRange,SnpSet,RangedDataCNV-method	RangedDataCNV-classes
ffdf-class	ffdf
ff_matrix-class	ff_matrix
ff_or_matrix-class	ff_or_matrix-class
findOverlaps	findOverlaps
findOverlaps,AnnotatedDataFrame,RangedDataCNV-method	findOverlaps
findOverlaps,RangedDataCNV,AnnotatedDataFrame-method	findOverlaps
findOverlaps,RangedDataCNV,CNSet-method	findOverlaps
findOverlaps,RangedDataCNV,RangedDataCNV-method	findOverlaps
findOverlaps,RangedDataCNV,SnpSet-method	findOverlaps
findOverlaps,RangedDataHMM,RangedDataHMM-method	findOverlaps
flags	flags
flags,AssayData-method	AssayData-methods
flags,CNSet-method	CNSet-class
GeneFeatureSet	FeatureSetExtensions-class
GeneFeatureSet-class	FeatureSetExtensions-class
GenomeAnnotatedDataFrame	GenomeAnnotatedDataFrame-class
GenomeAnnotatedDataFrame-class	GenomeAnnotatedDataFrame-class
GenomeAnnotatedDataFrameFrom	GenomeAnnotatedDataFrameFrom-methods
GenomeAnnotatedDataFrameFrom,AssayData-method	GenomeAnnotatedDataFrameFrom-methods
GenomeAnnotatedDataFrameFrom,ff_or_matrix-method	GenomeAnnotatedDataFrameFrom-methods
GenomeAnnotatedDataFrameFrom,NULL-method	GenomeAnnotatedDataFrameFrom-methods
genomeBuild	genomeBuild
genomeBuild,DBPDInfo-method	genomeBuild
genomeBuild,FeatureSet-method	genomeBuild
genomeBuild,gSet-method	gSet-class
geometry	geometry-methods
geometry,DBPDInfo-method	geometry-methods
geometry,FeatureSet-method	geometry-methods
getA	AlleleSet-methods
getA,AlleleSet-method	AlleleSet-class
getA,SnpCnvQSet-method	AlleleSet-methods
getA,SnpQSet-method	AlleleSet-methods
getA,TilingFeatureSet2-method	AlleleSet-methods
getBar	getBar
getCluster	clusterOptsDeprecated
getCluster-deprecated	clusterOptsDeprecated
getM	AlleleSet-methods
getM,AlleleSet-method	AlleleSet-class
getM,SnpCnvQSet-method	AlleleSet-methods
getM,SnpQSet-method	AlleleSet-methods
getM,TilingFeatureSet2-method	AlleleSet-methods
gSet	gSet-class
gSet-class	gSet-class
i2p	i2p_p2i
initialize,BeadStudioSet-method	BeadStudioSet-class
initialize,CNSet-method	CNSet-class
initialize,CNSetLM-method	CNSet-class
initialize,CopyNumberSet-method	CopyNumberSet-class
initialize,DBPDInfo-method	DBPDInfo-class
initialize,FeatureSet-method	FeatureSetExtensions-class
initialize,GenomeAnnotatedDataFrame-method	GenomeAnnotatedDataFrame-class
initialize,oligoSnpSet-method	oligoSnpSet-methods
initialize,SnpSuperSet-method	SnpSuperSet-class
initializeBigArray	largeObjects
initializeBigMatrix	largeObjects
initializeBigVector	largeObjects
integerArray	integerMatrix
integerMatrix	integerMatrix
is.ffmatrix	is.ffmatrix
isPackageLoaded	isPackageLoaded
isSnp	isSnp-methods
isSnp,character-method	isSnp-methods
isSnp,GenomeAnnotatedDataFrame-method	isSnp-methods
isSnp,gSet-method	isSnp-methods
isSnp,SnpSet-method	isSnp-methods
isSnp-methods	isSnp-methods
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
ldPath	ldOpts
ldSetOptions	ldOpts
ldStatus	ldOpts
length,FeatureSet-method	length-methods
length-methods	length-methods
library2	library2
list.celfiles	list.celfiles
list_or_ffdf-class	ffdf
locusLevelData	locusLevelData
lrr	generics
lrr,BeadStudioSet-method	BeadStudioSet-class
lrr<-	BeadStudioSet-class
lrr<-,BeadStudioSet-method	BeadStudioSet-class
manufacturer	manufacturer-methods
manufacturer,DBPDInfo-method	manufacturer-methods
manufacturer,FeatureSet-method	manufacturer-methods
manufacturer-methods	manufacturer-methods
mean,RangedDataCBS-method	RangedDataCNV-classes
NgsExpressionPDInfo	DBPDInfo-class
NgsExpressionPDInfo-class	DBPDInfo-class
NgsTilingPDInfo	DBPDInfo-class
NgsTilingPDInfo-class	DBPDInfo-class
nu	AssayData-methods
nu,AssayData,character-method	AssayData-methods
nu,CNSet,character-method	CNSet-class
ocLapply	ocLapply
ocProbesets	clusterOpts
ocSamples	clusterOpts
oligoSet	oligoSetExample
oligoSnpSet-class	oligoSnpSet-methods
open	fileConnections
open,AlleleSet-method	AlleleSet-methods
open,array-method	fileConnections
open,CNSet-method	CNSet-class
open,matrix-method	fileConnections
open,numeric-method	fileConnections
openff	fileConnections
openff,CNSet-method	fileConnections
p2i	i2p_p2i
parStatus	parStatus
pdPkgFromBioC	pdPkgFromBioC
phi	AssayData-methods
phi,AssayData,character-method	AssayData-methods
phi,CNSet,character-method	CNSet-class
platform	platform-methods
platform,FeatureSet-method	platform-methods
platform-methods	platform-methods
pmFragmentLength	pmFragmentLength-methods
pmFragmentLength,AffySNPPDInfo-method	pmFragmentLength-methods
pmFragmentLength-methods	pmFragmentLength-methods
position	position-methods
position,AnnotatedDataFrame-method	position-methods
position,GenomeAnnotatedDataFrame-method	position-methods
position,gSet-method	position-methods
position,SnpSet-method	position-methods
position-methods	position-methods
position<-	GenomeAnnotatedDataFrame-class
position<-,GenomeAnnotatedDataFrame,integer-method	GenomeAnnotatedDataFrame-class
position<-,oligoSnpSet,integer-method	oligoSnpSet-methods
RangedDataCBS	RangedDataCNV-utils
RangedDataCBS-class	RangedDataCNV-classes
RangedDataCNV	RangedDataCNV-utils
RangedDataCNV-class	RangedDataCNV-classes
RangedDataCopyNumber	RangedDataCNV-classes
RangedDataCopyNumber-class	RangedDataCNV-classes
RangedDataHMM	RangedDataCNV-utils
RangedDataHMM-class	RangedDataCNV-classes
requireAnnotation	requireAnnotation
requireClusterPkg	requireClusterPkgSetDeprecated
requireClusterPkg-deprecated	requireClusterPkgSetDeprecated
requireClusterPkgSet	requireClusterPkgSetDeprecated
requireClusterPkgSet-deprecated	requireClusterPkgSetDeprecated
sampleNames,FeatureSet-method	sampleNames-methods
sampleNames,RangedDataCNV-method	RangedDataCNV-classes
sampleNames-methods	sampleNames-methods
sampleNames<-,RangedDataCNV,character-method	RangedDataCNV-classes
scqsExample	data-scqsExample
se.exprs,FeatureSet-method	exprs-methods
setCluster	clusterOptsDeprecated
setCluster-deprecated	clusterOptsDeprecated
sfsExample	data-sfsExample
show,BeadStudioSet-method	BeadStudioSet-class
show,CNSet-method	CNSet-class
show,DBPDInfo-method	DBPDInfo-class
show,FeatureSet-method	FeatureSetExtensions-class
sigma2,CNSet,character-method	CNSet-class
snpCallProbability,CNSet-method	CNSet-class
SnpCnvFeatureSet	FeatureSetExtensions-class
SnpCnvFeatureSet-class	FeatureSetExtensions-class
SNPCNVPDInfo	DBPDInfo-class
SNPCNVPDInfo-class	DBPDInfo-class
SnpFeatureSet	FeatureSetExtensions-class
SnpFeatureSet-class	FeatureSetExtensions-class
SNPPDInfo	DBPDInfo-class
SNPPDInfo-class	DBPDInfo-class
SnpSuperSet	SnpSuperSet-class
SnpSuperSet-class	SnpSuperSet-class
splitIndicesByLength	splitVec
splitIndicesByNode	splitVec
sqsExample	data-sqsExample
state	RangedDataCNV-classes
state,RangedDataCNV-method	RangedDataCNV-classes
tau2,CNSet,character-method	CNSet-class
TilingFeatureSet	FeatureSetExtensions-class
TilingFeatureSet-class	FeatureSetExtensions-class
TilingFeatureSet2	FeatureSetExtensions-class
TilingFeatureSet2-class	FeatureSetExtensions-class
TilingPDInfo	DBPDInfo-class
TilingPDInfo-class	DBPDInfo-class
todf,RangedDataCNV,ANY-method	RangedDataCNV-classes
updateObject,BeadStudioSet-method	BeadStudioSet-class
updateObject,CNSet-method	CNSet-class
updateObject,GenomeAnnotatedDataFrame-method	GenomeAnnotatedDataFrame-class
updateObject,oligoSnpSet-method	oligoSnpSet-methods
[,CNSet-method	CNSet-class
