cbind.SegList	cbind
chrominfo.Mb	chrominfo.Mb
combine.func	mergeStates
compareBreakPoints	compareSegmentations
compareSegmentations	compareSegmentations
convert.output	convert.output
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
findBreakPoints	findBreakPoints
fit.model	fit.model
floor.func	heatmapGenome
generate.data	sim.structure
genomePlot	genomePlot
heatmapGenome	heatmapGenome
IDProbes	IDProbes
imputeMissingValues	imputeMissingValues
LargeDataObject-class	LargeDataObject
length.MAList	dim
length.RGList	dim
length.SegList	dim
log2ratios	log2ratios
maPalette	heatmapGenome
MergeLevels.new	mergeStates
MergeLevels.old	mergeStates
mergeStates	mergeStates
non.zero.length.distr.non.tiled	non.zero.length.distr.non.tiled
non.zero.length.distr.tiled	non.zero.length.distr.tiled
nudSegmentation	nudSegmentation
plotChrom	heatmapGenome
plotSegmentedGenome	plotSegmentedGenome
plotValChrom	heatmapGenome
plotvalChrom.func	heatmapGenome
plotValGenome	heatmapGenome
print.SegList	SegList
processCGH	processCGH
rbind.SegList	cbind
read.clonesinfo	read.clonesinfo
readPositionalInfo	readPositionalInfo
removeByWeights	removeByWeights
run.nelder	fit.model
runBioHMM	runBioHMM
runDNAcopy	runDNAcopy
runGLAD	runGLAD
runHomHMM	runHMM
runPicard	runPicard
sample.names	genomePlot
SegList-class	SegList
show,LargeDataObject-method	LargeDataObject
simulateData	sim.structure
states.hmm.func	runHMM
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
zoomChromosome	zoomChromosome
zoomGenome	zoomGenome
[.SegList	subsetting
