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| CHAT-package | Clonal Heterogeneity Analysis Tool |
| 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 | Clonal Heterogeneity Analysis Tool |
| Dist | Distance from point to a line |
| DPfitSamples | MCMC fitting of sAGP values |
| findRobustPeaks | Find well-separated peaks |
| getAGP | AGP estimation main function |
| getAmpDel | Fraction of amplification or deletion in the genome |
| getBAFmean | Compute mean of BAF |
| getCanonicalLines | Regression lines on canonical points with same number of minor alleles |
| getCCF | CCF estimation main function |
| getCoord | Computes coordinates of a canonical point |
| getCosine | Computes cosine value of the angle for two vectors. |
| getDiploidOrigin | Estimate diploid origin in higher ploidy samples |
| getDistToPath | Find nearest distance from a data point to a canonical line |
| getDPfit | MCMC fitting for single sample |
| 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 |
| getsAGP | Segment-specific AGP estimation main function |
| 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 |
| is.nearCP | Near canonical position |
| mcmc | MCMC parameters. |
| MergeBreakPointsByChr | Merge break points from two sets |
| NormalizeLRR | Normalize LRR values |
| plotBAFLRR | BAF-LRR plot |
| plotIdentifiableZone | Plot Identifiable Zone on sAGP-SAF plot |
| prior | Prior parameters for MCMC |
| SampleNMM | Normal-Uniform mixture model fitting |