cbind.SegList	cbind
changeProp.func	plotGainLoss
changeProp.overall.func	plotGainLoss
chrominfo.Mb	chrominfo.Mb
combine.func	mergeStates
computeSD	computeSD
convert.output	convert.output
create.resT	plotGainLoss
dim.MAList	dim
dim.RGList	dim
dim.SegList	dim
dimnames.SegList	dimnames
filterClones	filter
find.param.five	find.param.five
find.param.four	find.param.four
find.param.one	find.param.one
find.param.three	find.param.three
find.param.two	find.param.two
findAberrations	findAberrations
findAmplifications	findAmplifications
findBreakPoints	findBreakPoints
findGenomicEvents	findGenomicEvents
findOutliers	findOutliers
findTranslocations	findTranslocations
fit.model	fit.model
fitBioHMM	fitBioHMM
floor.func	heatmapGenome
fractionAltered	fractionAltered
GEList-class	GEList
genomePlot	genomePlot
heatmapGenome	heatmapGenome
imputeMissingValues	impute.lowess
LargeDataObject-class	LargeDataObject
length.MAList	dim
length.RGList	dim
length.SegList	dim
lengthGain.na	plotGainLoss
lengthLoss.na	plotGainLoss
log2ratios	log2ratios
maPalette	heatmapGenome
MergeLevels.new	mergeStates
MergeLevels.old	mergeStates
mergeStates	mergeStates
mod.chrominfo	mod.chrominfo
mu1.func	fitHMM
non.zero.length.distr.non.tiled	non.zero.length.distr.non.tiled
non.zero.length.distr.tiled	non.zero.length.distr.tiled
plotChrom	heatmapGenome
plotGainLoss	plotGainLoss
plotSegmentationStates	plotSegmentationStates
plotSegmentationSummary	plotSummaryProfile
plotSegmentedGenome	plotSegmentedGenome
plotValChrom	heatmapGenome
plotvalChrom.func	heatmapGenome
plotValGenome	heatmapGenome
print.SegList	SegList
processCGH	processCGH
prop.na	plotGainLoss
prop.num.func	plotSummaryProfile
propGain.na	plotGainLoss
propLoss.na	plotGainLoss
read.clonesinfo	read.clonesinfo
removeByWeights	removeByWeights
run.nelder	fit.model
runDNAcopy	runDNAcopy
runGLAD	runGLAD
runHomHMM	fitHMM
sample.names	genomePlot
SegList-class	SegList
show,LargeDataObject-method	LargeDataObject
sim.structure	sim.structure
states.hmm.func	fitHMM
summarizeClones	summarize.clones
table.bac.func	plotGainLoss
threshold	threshold.func
Viterbi.five	Viterbi.five
Viterbi.four	Viterbi.four
Viterbi.three	Viterbi.three
Viterbi.two	Viterbi.two
zero.length.distr.non.tiled	zero.length.distr.non.tiled
zero.length.distr.tiled	zero.length.distr.tiled
[.SegList	subsetting
