aCGH                    Class aCGH
aCGH.process            Process data in aCGH object
aCGH.read.Sprocs        Create object of class "aCGH" from Sproc files
aCGH.test               Testing association of aCGH clones with
                        censored or continuous outcomes
clusterGenome           clustering and heatmap
colorectal              Colorectal array CGH dataset
computeSD.func          Function to estimate experimental variability
                        of a sample
fga.func                Function to compute fraction of genome altered
                        for each sample
find.genomic.events     Finds the genomic events associated with each
                        of the array CGH samples
find.hmm.states         Determines states of the clones
findAber.func           Function to determines focal aberrations
findAmplif.func         Function to determine high level amplifications
findOutliers.func       Function to identify outlier clones
findTrans.func          Funtion identifying the transitions
gainLoss                Function to compute proportion of gains and
                        losses for each clones
heatmap                 Creates heatmap array CGH objects
human.chrom.info.Jul03
                        Basic Chromosomal Information for UCSC Human
                        Genome Assembly July 2003 freeze
human.chrom.info.May04
                        Basic Chromosomal Information for UCSC Human
                        Genome Assembly May 2004 freeze
impute.HMM              Imputing log2 ratios using HMM
impute.lowess           Imputing log2 ratios
mergeFunc               Funtion to merge states based on their state
                        means
mergeLevels             mergeLevels
plotFreqStat            frequency plots and significance analysis
plotGenome              Plots the genome
plotHmmStates           Plotting the estimated hmm states and log2
                        ratios for each sample.
plotSummaryProfile      plotSummaryProfile
states.hmm.func         A function to fit unsupervised Hidden Markov
                        model
summarize.clones        Extracting summary information for all clones
threshold.func          Function to indicate gain or loss for each
                        clone for each sample
