$,gSetList-method	gSetList-class
$<-,gSetList-method	gSetList-class
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
annotation,gSetList-method	gSetList-class
annotationPackages	annotationPackages
AssayDataList	AssayDataList
assayDataList	assayDataList-methods
assayDataList,gSetList-method	gSetList-class
assayDataList,oligoSetList-method	assayDataList-methods
assayDataList-methods	assayDataList-methods
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,BafLrrSetList-method	BeadStudioSetList-class
baf,BeadStudioSet-method	BeadStudioSet-class
baf,BeadStudioSetList-method	BeadStudioSetList-class
baf,oligoSetList-method	BeadStudioSetList-class
baf,oligoSnpSet-method	oligoSnpSet-methods
baf,RangedSummarizedExperiment-method	SummarizedExperiment-methods
baf,SummarizedExperiment-method	SummarizedExperiment-methods
baf<-	BeadStudioSet-class
baf<-,BeadStudioSet-method	BeadStudioSet-class
baf<-,oligoSnpSet-method	oligoSnpSet-methods
BafLrrSet-class	BeadStudioSet-class
BafLrrSetList-class	BeadStudioSetList-class
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
BeadStudioSetList-class	BeadStudioSetList-class
bothStrands	AlleleSet-class
bothStrands,AlleleSet-method	AlleleSet-class
bothStrands,SnpFeatureSet-method	AlleleSet-class
calls	SnpSet-methods
calls,CNSet-method	CNSet-class
calls,oligoSetList-method	BeadStudioSetList-class
calls,oligoSnpSet-method	oligoSnpSet-methods
calls,SnpSet-method	SnpSet-methods
calls,SnpSet2-method	SnpSet2-class
calls<-	SnpSet-methods
calls<-,CNSet,matrix-method	CNSet-class
calls<-,oligoSnpSet,matrix-method	oligoSnpSet-methods
calls<-,SnpSet,matrix-method	SnpSet-methods
calls<-,SnpSet2,matrix-method	SnpSet2-class
callsConfidence,oligoSnpSet-method	oligoSnpSet-methods
callsConfidence<-,oligoSnpSet,matrix-method	oligoSnpSet-methods
celfileDate	celfileDate
celfileName	celfileName
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,GRanges-method	chromosome-methods
chromosome,GRangesList-method	chromosome-methods
chromosome,gSet-method	chromosome-methods
chromosome,gSetList-method	gSetList-class
chromosome,RangedDataCNV-method	defunct
chromosome,RangedSummarizedExperiment-method	SummarizedExperiment-methods
chromosome,SnpSet-method	chromosome-methods
chromosome,SummarizedExperiment-method	SummarizedExperiment-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
clone2	BeadStudioSetList-class
clone2,BafLrrSetList-method	BeadStudioSetList-class
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,gSetList,list-method	gSetList-class
coerce,oligoSnpSet,data.frame-method	oligoSnpSet-methods
confs	SnpSet-methods
confs,CNSet-method	CNSet-class
confs,SnpSet-method	SnpSet-methods
confs,SnpSet2-method	SnpSet2-class
confs<-	SnpSet-methods
confs<-,CNSet,matrix-method	CNSet-class
confs<-,SnpSet,matrix-method	SnpSet-methods
confs<-,SnpSet2,matrix-method	SnpSet2-class
copyNumber	CopyNumberSet-methods
copyNumber,BeadStudioSet-method	BeadStudioSet-class
copyNumber,CopyNumberSet-method	CopyNumberSet-class
copyNumber,oligoSetList-method	BeadStudioSetList-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	GRanges-methods
coverage2,GRanges-method	GRanges-methods
coverage2,GRangesList-method	GRanges-methods
coverage2,RangedDataCNV-method	defunct
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
dims,gSetList-method	gSetList-class
efsExample	data-efsExample
elementNROWS,gSetList-method	gSetList-class
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,SnpSet2-method	SnpSet2-class
exprs-methods	exprs-methods
featureDataList	featureDataList-methods
featureDataList,gSetList-method	gSetList-class
featureDataList-methods	featureDataList-methods
FeatureSet	FeatureSetExtensions-class
FeatureSet-class	FeatureSetExtensions-class
featuresInRange	defunct
featuresInRange,SnpSet2,RangedDataCNV-method	defunct
ffdf-class	ffdf
ff_matrix-class	ff_matrix
ff_or_matrix-class	ff_or_matrix-class
findOverlaps,AnnotatedDataFrame,RangedDataCNV-method	defunct
findOverlaps,GRanges,gSet-method	GRanges-methods
findOverlaps,GRangesList,gSet-method	GRanges-methods
findOverlaps,RangedDataCNV,AnnotatedDataFrame-method	defunct
findOverlaps,RangedDataCNV,CNSet-method	defunct
findOverlaps,RangedDataCNV,RangedDataCNV-method	defunct
findOverlaps,RangedDataCNV,SnpSet-method	defunct
findOverlaps,RangedDataHMM,RangedDataHMM-method	defunct
flags	flags
flags,AssayData-method	AssayData-methods
flags,CNSet-method	CNSet-class
GeneFeatureSet	FeatureSetExtensions-class
GeneFeatureSet-class	FeatureSetExtensions-class
GenericFeatureSet	FeatureSetExtensions-class
GenericFeatureSet-class	FeatureSetExtensions-class
GenericPDInfo	DBPDInfo-class
GenericPDInfo-class	DBPDInfo-class
GenomeAnnotatedDataFrame	GenomeAnnotatedDataFrame-class
GenomeAnnotatedDataFrame-class	GenomeAnnotatedDataFrame-class
GenomeAnnotatedDataFrameFrom	GenomeAnnotatedDataFrameFrom-methods
GenomeAnnotatedDataFrameFrom,array-method	GenomeAnnotatedDataFrameFrom-methods
GenomeAnnotatedDataFrameFrom,AssayData-method	GenomeAnnotatedDataFrameFrom-methods
GenomeAnnotatedDataFrameFrom,ff_or_matrix-method	GenomeAnnotatedDataFrameFrom-methods
GenomeAnnotatedDataFrameFrom,list-method	GenomeAnnotatedDataFrameFrom-methods
GenomeAnnotatedDataFrameFrom,NULL-method	GenomeAnnotatedDataFrameFrom-methods
genomeBuild	genomeBuild
genomeBuild,DBPDInfo-method	genomeBuild
genomeBuild,FeatureSet-method	genomeBuild
genomeBuild,GRanges-method	GRanges-methods
genomeBuild,gSet-method	gSet-class
genomeBuild,gSetList-method	gSetList-class
genomeBuild<-	genomeBuild
genomeBuild<-,gSet,character-method	gSet-class
genomeBuild<-,gSetList,character-method	gSetList-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
getArm	gSet-class
getArm,GenomeAnnotatedDataFrame-method	GenomeAnnotatedDataFrame-class
getArm,gSet-method	gSet-class
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
getSequenceLengths	getSequenceLengths
gSet	gSet-class
gSet-class	gSet-class
gSetList-class	gSetList-class
i2p	i2p_p2i
initialize,BeadStudioSet-method	BeadStudioSet-class
initialize,BeadStudioSetList-method	BeadStudioSetList-class
initialize,CNSet-method	CNSet-class
initialize,CNSetLM-method	CNSet-class
initialize,CopyNumberSet-method	CopyNumberSet-class
initialize,DBPDInfo-method	DBPDInfo-class
initialize,eSetList-method	ClassesNotExported
initialize,FeatureSet-method	FeatureSetExtensions-class
initialize,GenomeAnnotatedDataFrame-method	GenomeAnnotatedDataFrame-class
initialize,gSet-method	gSet-class
initialize,gSetList-method	gSetList-class
initialize,oligoSnpSet-method	oligoSnpSet-methods
initialize,SnpSet2-method	SnpSet2-class
initialize,SnpSuperSet-method	SnpSuperSet-class
initializeBigArray	largeObjects
initializeBigMatrix	largeObjects
initializeBigVector	largeObjects
integer2chromosome	chromosome2integer
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,RangedSummarizedExperiment-method	SummarizedExperiment-methods
isSnp,SnpSet-method	isSnp-methods
isSnp,SummarizedExperiment-method	SummarizedExperiment-methods
isSnp-methods	isSnp-methods
kind	kind
kind,AffyExonPDInfo-method	kind
kind,AffyExpressionPDInfo-method	kind
kind,AffyGenePDInfo-method	kind
kind,AffyHTAPDInfo-method	kind
kind,AffySNPCNVPDInfo-method	kind
kind,AffySNPPDInfo-method	kind
kind,ExpressionPDInfo-method	kind
kind,FeatureSet-method	kind
kind,GenericPDInfo-method	kind
kind,TilingPDInfo-method	kind
ldPath	ldOpts
ldSetOptions	ldOpts
ldStatus	ldOpts
length,FeatureSet-method	length-methods
length,gSetList-method	gSetList-class
length-methods	length-methods
library2	library2
list.celfiles	list.celfiles
list_or_ffdf-class	ffdf
locusLevelData	locusLevelData
lrr	generics
lrr,BafLrrSetList-method	BeadStudioSetList-class
lrr,BeadStudioSet-method	BeadStudioSet-class
lrr,BeadStudioSetList-method	BeadStudioSetList-class
lrr,RangedSummarizedExperiment-method	SummarizedExperiment-methods
lrr,SummarizedExperiment-method	SummarizedExperiment-methods
lrr<-	BeadStudioSet-class
lrr<-,BafLrrSet,ANY-method	BeadStudioSet-class
lrr<-,BafLrrSet-method	BeadStudioSet-class
lrr<-,BafLrrSetList,matrix-method	BeadStudioSetList-class
lrr<-,BeadStudioSet,ANY-method	BeadStudioSet-class
lrr<-,BeadStudioSet-method	BeadStudioSet-class
makeFeatureGRanges	makeFeatureGRanges
makeFeatureGRanges,GenomeAnnotatedDataFrame-method	GenomeAnnotatedDataFrame-class
makeFeatureGRanges,gSet-method	gSet-class
makeFeatureGRanges,gSetList-method	gSetList-class
manufacturer	manufacturer-methods
manufacturer,DBPDInfo-method	manufacturer-methods
manufacturer,FeatureSet-method	manufacturer-methods
manufacturer-methods	manufacturer-methods
mean,RangedDataCBS-method	defunct
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
numberProbes	GRanges-methods
numberProbes,GRanges-method	GRanges-methods
numberProbes,GRangesList-method	GRanges-methods
ocLapply	ocLapply
ocProbesets	clusterOpts
ocSamples	clusterOpts
oligoSet	oligoSetExample
oligoSetList-class	BeadStudioSetList-class
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,gSetList-method	gSetList-class
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	defunct
RangedDataCBS-class	defunct
RangedDataCNV	defunct
RangedDataCNV-class	defunct
RangedDataCopyNumber-class	defunct
RangedDataHMM	defunct
RangedDataHMM-class	defunct
requireAnnotation	requireAnnotation
requireClusterPkg	requireClusterPkgSetDeprecated
requireClusterPkg-deprecated	requireClusterPkgSetDeprecated
requireClusterPkgSet	requireClusterPkgSetDeprecated
requireClusterPkgSet-deprecated	requireClusterPkgSetDeprecated
sampleNames,FeatureSet-method	sampleNames-methods
sampleNames,GRanges-method	GRanges-methods
sampleNames,GRangesList-method	GRanges-methods
sampleNames,gSetList-method	gSetList-class
sampleNames,RangedDataCNV-method	defunct
sampleNames-methods	sampleNames-methods
sampleNames<-,gSetList,character-method	gSetList-class
sampleNames<-,RangedDataCNV,character-method	defunct
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
show,gSet-method	gSet-class
show,gSetList-method	gSetList-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
SnpSet2-class	SnpSet2-class
SnpSuperSet	SnpSuperSet-class
SnpSuperSet-class	SnpSuperSet-class
splitIndicesByLength	splitVec
splitIndicesByNode	splitVec
sqsExample	data-sqsExample
state	GRanges-methods
state,GRanges-method	GRanges-methods
state,GRangesList-method	GRanges-methods
state,RangedDataCNV-method	defunct
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
updateObject,BeadStudioSet-method	BeadStudioSet-class
updateObject,BeadStudioSetList-method	BeadStudioSetList-class
updateObject,CNSet-method	CNSet-class
updateObject,GenomeAnnotatedDataFrame-method	GenomeAnnotatedDataFrame-class
updateObject,oligoSnpSet-method	oligoSnpSet-methods
[,CNSet,ANY-method	CNSet-class
[,CNSet-method	CNSet-class
[,gSetList,ANY-method	gSetList-class
[,gSetList-method	gSetList-class
[[,BafLrrSetList,ANY,ANY-method	BeadStudioSetList-class
[[,BeadStudioSetList,ANY,ANY-method	BeadStudioSetList-class
[[<-,BafLrrSetList,ANY,ANY,BafLrrSet-method	BeadStudioSetList-class
[[<-,gSetList,ANY,ANY,BafLrrSet-method	gSetList-class
