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
addFeatureAnnotation	addFeatureAnnotation
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
allele	AlleleSet-class
allele,AlleleSet-method	AlleleSet-class
allele,CNSet-method	CNSet-class
allele,SnpFeatureSet-method	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
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
bothStrands	AlleleSet-class
bothStrands,AlleleSet-method	AlleleSet-class
bothStrands,SnpFeatureSet-method	AlleleSet-class
calls	SnpSet-methods
calls,oligoSnpSet-method	oligoSnpSet-methods
calls,SnpSet-method	SnpSet-methods
calls<-	SnpSet-methods
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,SnpSet-method	SnpSet-methods
chromosome	eSet-methods
chromosome,AnnotatedDataFrame-method	eSet-methods
chromosome,eSet-method	eSet-methods
chromosome,RangedDataCNV-method	RangedDataCNV-classes
chromosome2integer	chromosome2integer
chromosome<-	eSet-methods
chromosome<-,eSet-method	eSet-methods
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-class	CNSet-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-utils
coerce,RangedData,RangedDataHMM-method	RangedDataCNV-utils
confs	SnpSet-methods
confs,SnpSet-method	SnpSet-methods
confs<-	SnpSet-methods
confs<-,SnpSet,matrix-method	SnpSet-methods
copyNumber	CopyNumberSet-methods
copyNumber,CopyNumberSet-method	CopyNumberSet-class
copyNumber,oligoSnpSet-method	oligoSnpSet-methods
copyNumber<-	CopyNumberSet-methods
copyNumber<-,CopyNumberSet,matrix-method	CopyNumberSet-class
copyNumber<-,oligoSnpSet,matrix-method	oligoSnpSet-methods
CopyNumberSet-class	CopyNumberSet-class
CopyNumberSet-methods	CopyNumberSet-methods
corr	AssayData-methods
corr,CNSet,character-method	CNSet-class
coverage2	RangedDataCNV-utils
coverage2,RangedDataCNV-method	RangedDataCNV-classes
createFF	createFF
db	db
db,AlleleSet-method	AlleleSet-class
db,DBPDInfo-method	db
db,eSet-method	db
db,FeatureSet-method	db
db,SnpCnvQSet-method	db
db,SnpQSet-method	db
db-methods	db
DBPDInfo-class	DBPDInfo-class
delCluster	clusterOpts
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
featuresInRange	featuresInRange
featuresInRange,SnpSet,RangedDataCNV-method	RangedDataCNV-classes
ffdf-class	ffdf
ff_matrix-class	ff_matrix
findOverlaps	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-class	FeatureSetExtensions-class
genomeBuild	genomeBuild
genomeBuild,DBPDInfo-method	genomeBuild
genomeBuild,FeatureSet-method	genomeBuild
geometry	PDInfo-methods
geometry,DBPDInfo-method	PDInfo-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	clusterOpts
getM	AlleleSet-methods
getM,AlleleSet-method	AlleleSet-class
getM,SnpCnvQSet-method	AlleleSet-methods
getM,SnpQSet-method	AlleleSet-methods
getM,TilingFeatureSet2-method	AlleleSet-methods
i2p	i2p_p2i
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,oligoSnpSet-method	oligoSnpSet-methods
initialize,SnpSuperSet-method	SnpSuperSet-class
initializeBigMatrix	largeObjects
initializeBigVector	largeObjects
is.ffmatrix	is.ffmatrix
isPackageLoaded	isPackageLoaded
isSnp	eSet-methods
isSnp,character,character-method	eSet-methods
isSnp,eSet,ANY-method	eSet-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
list.celfiles	list.celfiles
list_or_ffdf-class	ffdf
locusLevelData	locusLevelData
lrr	generics
manufacturer	manufacturer-methods
manufacturer,DBPDInfo-method	manufacturer-methods
manufacturer,FeatureSet-method	manufacturer-methods
manufacturer-methods	manufacturer-methods
NgsExpressionPDInfo-class	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
order	order
order,CopyNumberSet-method	order
order,SnpSet-method	order
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	eSet-methods
position,AnnotatedDataFrame-method	eSet-methods
position,eSet-method	eSet-methods
RangedDataCBS	RangedDataCNV-utils
RangedDataCBS-class	RangedDataCNV-classes
RangedDataCNV	RangedDataCNV-utils
RangedDataCNV-class	RangedDataCNV-classes
RangedDataCopyNumber-class	RangedDataCNV-classes
RangedDataHMM	RangedDataCNV-utils
RangedDataHMM-class	RangedDataCNV-classes
requireAnnotation	requireAnnotation
requireClusterPkg	requireClusterPkgSet
requireClusterPkgSet	requireClusterPkgSet
sampleNames,FeatureSet-method	sampleNames-methods
sampleNames,RangedDataCNV-method	RangedDataCNV-classes
sampleNames-methods	sampleNames-methods
sampleNames<-,RangedDataCNV,character-method	RangedDataCNV-utils
scqsExample	data-scqsExample
se.exprs,FeatureSet-method	exprs-methods
setCluster	clusterOpts
sfsExample	data-sfsExample
show,CNSet-method	CNSet-class
show,DBPDInfo-method	DBPDInfo-class
show,FeatureSet-method	FeatureSetExtensions-class
sigma2,CNSet,character-method	CNSet-class
SnpCnvFeatureSet-class	FeatureSetExtensions-class
SNPCNVPDInfo-class	DBPDInfo-class
SnpFeatureSet-class	FeatureSetExtensions-class
SNPPDInfo-class	DBPDInfo-class
SnpSuperSet-class	SnpSuperSet-class
splitIndicesByLength	splitVec
splitIndicesByNode	splitVec
sqsExample	data-sqsExample
state	RangedDataCNV-utils
state,RangedDataCNV-method	RangedDataCNV-classes
tau2,CNSet,character-method	CNSet-class
TilingFeatureSet-class	FeatureSetExtensions-class
TilingFeatureSet2-class	FeatureSetExtensions-class
TilingPDInfo-class	DBPDInfo-class
todf,RangedDataCNV,ANY-method	RangedDataCNV-classes
updateObject,CNSet-method	CNSet-class
[,CNSet-method	CNSet-class
