VanillaICE-package	VanillaICE
"[",ArrayViews,ANY-method	ArrayViews-class
$,ArrayViews-method	ArrayViews-class
$<-,ArrayViews-method	ArrayViews-class
'[',ArrayViews,ANY-method	ArrayViews-class
acf2	acf2
ArrayViews	ArrayViews-class
ArrayViews,numeric,numeric-method	ArrayViews-class
ArrayViews-class	ArrayViews-class
baf,ArrayViews-method	LowLevelSummaries
baf,SnpArrayExperiment-method	LowLevelSummaries
baf,SnpSet2-method	Defunct
bafFile	IO
bafFile,ArrayViews-method	IO
baf_means	EmissionParam-methods
baf_means,ArrayViews-method	ArrayViews-class
baf_means,EmissionParam-method	EmissionParam-methods
baf_means,HmmParam-method	EmissionParam-methods
baf_means<-	EmissionParam-methods
baf_means<-,EmissionParam,numeric-method	EmissionParam-methods
baf_sds	EmissionParam-methods
baf_sds,EmissionParam-method	EmissionParam-methods
baf_sds,HmmParam-method	EmissionParam-methods
baf_sds<-	EmissionParam-methods
baf_sds<-,EmissionParam,numeric-method	EmissionParam-methods
baumWelchUpdate	baumWelchUpdate
BeadStudioSet	BeadStudioSet
BeadStudioSetList	BeadStudioSet
BeadStudioSetList,BeadStudioSet-method	BeadStudioSet
BeadStudioSetList,character-method	BeadStudioSet
calculateEmission	calculateEmission
calculateEmission,list-method	calculateEmission
calculateEmission,numeric-method	calculateEmission
calculateEmission,RangedSummarizedExperiment-method	calculateEmission
cnvFilter	cnvFilter
cnvFilter,GRanges-method	cnvFilter
cnvFilter,HMM-method	cnvFilter
cnvFilter,HMMList-method	cnvFilter
cnvSegs	cnvFilter
cnvSegs,HMM-method	cnvFilter
cnvSegs,HmmGRanges-method	cnvFilter
cnvSegs,HMMList-method	cnvFilter
cn_means	EmissionParam-methods
cn_means,EmissionParam-method	EmissionParam-methods
cn_means,HmmParam-method	EmissionParam-methods
cn_means<-	EmissionParam-methods
cn_means<-,EmissionParam,numeric-method	EmissionParam-methods
cn_sds	EmissionParam-methods
cn_sds,EmissionParam-method	EmissionParam-methods
cn_sds,HmmParam-method	EmissionParam-methods
cn_sds<-	EmissionParam-methods
cn_sds<-,EmissionParam,numeric-method	EmissionParam-methods
colModes	robust-statistics
colnames	ArrayViews-class
colnames,ArrayViews-method	ArrayViews-class
colnames<-	ArrayViews-class
colnames<-,ArrayViews,character-method	ArrayViews-class
constrainMu2	constraints
constrainSd2	constraints
copyNumber,SnpArrayExperiment-method	LowLevelSummaries
copyNumberLimits	constraints
CopyNumScanParams	CopyNumScanParams
CopyNumScanParams-class	CopyNumScanParams
deletion	cnvFilter
deletion,HMM-method	cnvFilter
dim,ArrayViews-method	ArrayViews-class
doUpdate	doUpdate
dropDuplicatedMapLocs	dropDuplicatedMapLocs
dropSexChrom	dropSexChrom
duplication	cnvFilter
duplication,HMM-method	cnvFilter
duplication,HMMList-method	cnvFilter
emission	emission
emission,HmmParam-method	emission
emission<-	emission
emission<-,HMM-method	emission
emission<-,HmmParam-method	emission
EmissionParam	EmissionParam-methods
emissionParam	emissionParam
emissionParam,HMM-method	emissionParam
emissionParam,HmmGRanges-method	emissionParam
emissionParam,HmmParam-method	emissionParam
EmissionParam,missing-method	EmissionParam-methods
EmissionParam,numeric-method	EmissionParam-methods
emissionParam<-	emissionParam
emissionParam<-,HmmGRanges,EmissionParam-method	emissionParam
emissionParam<-,HmmParam,EmissionParam-method	emissionParam
EMupdates	EmissionParam-methods
EMupdates,EmissionParam-method	EmissionParam-methods
EMupdates,HmmParam-method	EmissionParam-methods
FilterParam	FilterParam-class
FilterParam-class	FilterParam-class
filters	filters
filters,HMM-method	filters
filters,HmmParam-method	filters
genotypes	LowLevelSummaries
genotypes,ArrayViews-method	LowLevelSummaries
genotypes,SnpArrayExperiment-method	LowLevelSummaries
getExampleSnpExperiment	getExampleSnpExperiment
getHmmParams	getHmmParams
getHmmParams,HMM-method	getHmmParams
getHmmParams,HmmParam-method	getHmmParams
gtFile	IO
gtFile,ArrayViews-method	IO
hemizygous	cnvFilter
hemizygous,HMM-method	cnvFilter
hemizygous,HMMList-method	cnvFilter
HMM	HMM
hmm	Deprecated
hmm,BafLrrSetList-method	Deprecated
hmm,BeadStudioSet-method	Deprecated
hmm,BeadStudioSetList-method	Deprecated
hmm,oligoSetList-method	Deprecated
hmm,oligoSnpSet-method	Deprecated
hmm,SnpSet2-method	Deprecated
HMM-class	HMM
hmm.setup	Defunct
hmm2	hmm2
hmm2,ArrayViews-method	hmm2
hmm2,oligoSnpSet-method	hmm2
hmm2,SnpArrayExperiment-method	hmm2
HMMList	HMMList
HMMList-class	HMMList-class
HmmOptionList	Defunct
HmmOptionList-class	Defunct
HmmParam	HmmParam
HmmParam,matrix-method	HmmParam
HmmParam,missing-method	HmmParam
hmmResults	hmmResults
HmmTrellisParam	HmmTrellisParam
homozygous	cnvFilter
homozygous,HMM-method	cnvFilter
homozygous,HMMList-method	cnvFilter
icePlatforms	icePlatforms
IdiogramParams	IdiogramParam-class
IdiogramParams-class	IdiogramParams-class
isHeterozygous	isHeterozygous
isHeterozygous,ArrayViews-method	isHeterozygous
isHeterozygous,matrix-method	isHeterozygous
isHeterozygous,numeric-method	isHeterozygous
isHeterozygous,SnpArrayExperiment-method	isHeterozygous
length,LogLik-method	LogLik-class
LogLik	LogLik
LogLik-class	LogLik-class
lrr,ArrayViews-method	LowLevelSummaries
lrr,SnpArrayExperiment-method	LowLevelSummaries
lrrFile	IO
lrrFile,ArrayViews-method	IO
lrrFile<-	IO
lrrFile<-,ArrayViews-method	IO
matrixOrNULL	matrixOrNULL-class
matrixOrNULL-class	matrixOrNULL-class
NA_filter	NA_filter
NA_filter,character-method	NA_filter
NA_filter,list-method	NA_filter
NA_filter,numeric-method	NA_filter
NA_filter,oligoSnpSet-method	NA_filter
NA_filter,SnpArrayExperiment-method	NA_filter
ncol,ArrayViews-method	ArrayViews-class
ncol,HmmParam-method	HmmParam
nrow,ArrayViews-method	ArrayViews-class
nrow,HmmParam-method	HmmParam
numberFeatures	numberFeatures
numberFeatures,FilterParam-method	numberFeatures
numberFeatures,HMM-method	numberFeatures
numberFeatures,HmmGRanges-method	numberFeatures
parsedPath	parsedPath
parsedPath,ArrayViews-method	parsedPath
parseSourceFile	parseSourceFile
parseSourceFile,ArrayViews,CopyNumScanParams-method	parseSourceFile
plot,IdiogramParams,ANY-method	IdiogramParam-class
plot,IdiogramParams-method	IdiogramParam-class
probability	probability
probability,FilterParam-method	FilterParam-class
read.bsfiles	read.bsfiles
rescale	rescale
robustSds	Deprecated
rowMAD	robust-statistics
rowModes	robust-statistics
sapply,ArrayViews-method	ArrayViews-class
segs	segs
segs,HMM-method	segs
segs,HMMList-method	cnvFilter
show,ArrayViews-method	ArrayViews-class
show,CopyNumScanParams-method	CopyNumScanParams
show,EmissionParam-method	EmissionParam-methods
show,FilterParam-method	FilterParam-class
show,HMM-method	HMM
show,HMMList-method	HMMList-class
show,HmmParam-method	HmmParam
show,IdiogramParams-method	IdiogramParams-class
show,LogLik-method	LogLik-class
show,TransitionParam-method	TransitionParam
show,Viterbi-method	Viterbi-methods
snpArrayAssays	snpArrayAssays
SnpArrayExperiment	SnpArrayExperiment-class
SnpArrayExperiment,matrix-method	SnpArrayExperiment-class
SnpArrayExperiment,missing-method	SnpArrayExperiment-class
SnpArrayExperiment-class	SnpArrayExperiment-class
SnpExperiment	SnpExperiment
SnpExperiment,ArrayViews-method	SnpExperiment
SnpGRanges	SnpGRanges
SnpGRanges,GRanges-method	SnpGRanges
SnpGRanges,missing-method	SnpGRanges
SnpGRanges-class	SnpGRanges
snp_exp	snp_exp
sourcePaths	sourcePaths
sourcePaths,ArrayViews-method	sourcePaths
start,ArrayViews-method	ArrayViews-class
start,oligoSnpSet-method	start-oligoSnpSet-method
state,FilterParam-method	FilterParam-class
state,HMM-method	HMM
state,HmmGRanges-method	HmmGRanges-methods
state,Viterbi-method	state-methods
state-methods	state-methods
sweepMode	sweepMode
sweepMode,SnpArrayExperiment-method	sweepMode
threshold	threshold
TransitionParam	TransitionParam
TransitionParam,missing-method	TransitionParam
TransitionParam,numeric-method	TransitionParam
unlist,HMMList-method	HMMList-class
updateHmmParams	updateHmmParams
VanillaICE	VanillaICE
viewports	viewports
viterbi2Wrapper	viterbi2Wrapper
xygrid	plotting
xyplotList	plotting
xyplotList,GRangesList,SnpArrayExperiment-method	plotting
xyplotList,HmmGRanges,SnpArrayExperiment-method	plotting
[,ArrayViews,ANY,ANY,ANY-method	ArrayViews-class
[[,oligoSetList,ANY,ANY-method	oligoSetList
