aCGH	aCGH
aCGH.process	aCGH.process
aCGH.read.Sprocs	aCGH.read.Sprocs
aCGH.test	aCGH.test
as.matrix.dist	find.hmm.states
changeProp.func	plotFreqStat
changeProp.overall.func	plotFreqStat
clone.names	aCGH
clone.names<-	aCGH
clones.info	aCGH
clones.info.ex	colorectal
clusterGenome	clusterGenome
col.names.aCGH	aCGH
col.names<-.aCGH	aCGH
colnames.aCGH	aCGH
colnames<-.aCGH	aCGH
colorectal	colorectal
combine.func	mergeLevels
computeSD.func	computeSD.func
computeSD.Samples	computeSD.func
corna	aCGH
create.aCGH	aCGH
create.resT	plotFreqStat
dim.aCGH	aCGH
dotify.names	aCGH.read.Sprocs
ex.acgh.hmm	aCGH
extract.clones.info	aCGH.read.Sprocs
fga.func	fga.func
find.genomic.events	find.genomic.events
find.hmm.states	find.hmm.states
findAber.func	findAber.func
findAmplif.func	findAmplif.func
findOutliers.func	findOutliers.func
findTrans.func	findTrans.func
floor.func	aCGH
gainLoss	gainLoss
genomic.events	aCGH
genomic.events<-	aCGH
heatmap	heatmap
hmm	aCGH
hmm.merged	aCGH
hmm.merged<-	aCGH
hmm.run.func	find.hmm.states
hmm<-	aCGH
human.chrom.info.Jul03	human.chrom.info.Jul03
human.chrom.info.May04	human.chrom.info.May04
impute.HMM	impute.HMM
impute.lowess	impute.lowess
is.aCGH	aCGH
length.num.func	aCGH
lengthGain.na	plotFreqStat
lengthLoss.na	plotFreqStat
log2.ratios	aCGH
log2.ratios.ex	colorectal
log2.ratios.imputed	aCGH
log2.ratios.imputed<-	aCGH
maPalette	plotGenome
maxdiff.func	aCGH.read.Sprocs
maxna	aCGH
mergeFunc	mergeFunc
mergeHmmStates	mergeFunc
mergeLevels	mergeLevels
mincorr.func	aCGH.read.Sprocs
minna	aCGH
mt.maxT	aCGH.test
mt.minP	aCGH.test
ncol.aCGH	aCGH
nrow.aCGH	aCGH
num.chromosomes	aCGH
num.clones	aCGH
num.samples	aCGH
pheno.type.ex	colorectal
phenotype	aCGH
phenotype<-	aCGH
plot.aCGH	aCGH
plotCGH.func	plotGenome
plotCGH.hmm.func	find.hmm.states
plotChrom	clusterGenome
plotChrom.grey.samples.func	find.hmm.states
plotChrom.hmm.func	find.hmm.states
plotChrom.samples.func	find.hmm.states
plotfreq.givenstat.final.colors.func	plotFreqStat
plotfreq.stat.chrom.final.func	plotFreqStat
plotfreq.stat.final.func	plotFreqStat
plotFreqGivenStat	plotFreqStat
plotfreqGivenStatFinalColors	plotFreqStat
plotFreqStat	plotFreqStat
plotFreqStatColors	plotFreqStat
plotFreqStatGrey	plotFreqStat
plotGene	plotGenome
plotGeneSign	plotGenome
plotGenome	plotGenome
plotHmmStates	plotHmmStates
plotHmmStatesNew	plotHmmStates
plotSummaryProfile	plotSummaryProfile
plotValChrom	clusterGenome
plotvalChrom.func	clusterGenome
plotValGenome	clusterGenome
print.aCGH	aCGH
prop.na	plotFreqStat
prop.num.func	aCGH
propGain.na	plotFreqStat
propLoss.na	plotFreqStat
read.Sproc.files	aCGH.read.Sprocs
row.names.aCGH	aCGH
row.names<-.aCGH	aCGH
rownames.aCGH	aCGH
rownames<-.aCGH	aCGH
sample.names	aCGH
sample.names<-	aCGH
sd.samples	aCGH
sd.samples<-	aCGH
smoothData.func	find.hmm.states
states.hmm.func	states.hmm.func
subset.hmm	aCGH
subset.hmm.merged	aCGH
summarize.clones	summarize.clones
summary.aCGH	aCGH
table.bac.func	plotFreqStat
threshold.func	threshold.func
thresholdData.func	find.hmm.states
[.aCGH	aCGH
