A0SD.BAF                B-allele frequencies of selected chromosomes
                        for TCGA sample A1-A0SD.
A0SD.LRR                Copy number information of selected chromosomes
                        for TCGA sample A1-A0SD.
ApproxBIC               Approximate BIC calculation
CHAT-package            Clonal Heterogeneity Analysis Tool
DPfitSamples            MCMC fitting of sAGP values
Dist                    Distance from point to a line
MergeBreakPointsByChr   Merge break points from two sets
NormalizeLRR            Normalize LRR values
SampleNMM               Normal-Uniform mixture model fitting
findRobustPeaks         Find well-separated peaks
getAGP                  AGP estimation main function
getAmpDel               Fraction of amplification or deletion in the
                        genome
getBAFmean              Compute mean of BAF
getCCF                  CCF estimation main function
getCanonicalLines       Regression lines on canonical points with same
                        number of minor alleles
getCoord                Computes coordinates of a canonical point
getCosine               Computes cosine value of the angle for two
                        vectors.
getDPfit                MCMC fitting for single sample
getDiploidOrigin        Estimate diploid origin in higher ploidy
                        samples
getDistToPath           Find nearest distance from a data point to a
                        canonical line
getGrid                 Find all the coordinates for canonical points
getHets                 Obtain germline heterozygous markers
getKmeans               K-means clustering of data points
getLOH                  Fraction of loss-of-heterozygosity
getOrigin               Inference of Origin Cluster
getPara                 Initialize parameters for AGP estimation
getPara.sAGP            Initialize parameters for sAGP estimation.
getPeaks                Find peaks on a curve
getPermutation          Null distribution for estimated AGP.
getPloidy               Genomewide average ploidy
getSampleAGP            AGP inference by sample
getSampleCCF            CCF estimation by sample.
getSeg                  Perform DNA segmentation and calculate folded
                        BAF and logR ratios.
getSegChr               Perform binned DNA segmentation by chromosome
getSegChr.CBS           Perform circular binary segmentation by
                        chromosome
getSegPurity            Segment-specific AGP inference by sample
getSumDist              Compute the summation of distances
getUnifiedMap           Merge adjacent break points
getsAGP                 Segment-specific AGP estimation main function
is.nearCP               Near canonical position
mcmc                    MCMC parameters.
plotBAFLRR              BAF-LRR plot
plotIdentifiableZone    Plot Identifiable Zone on sAGP-SAF plot
prior                   Prior parameters for MCMC
