Clonal Heterogeneity Analysis Tool

A0SD.BAF | B-allele frequencies of selected chromosomes for TCGA sample... |

A0SD.LRR | Copy number information of selected chromosomes for TCGA... |

ApproxBIC | Approximate BIC calculation |

CHAT-package | 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... |

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... |

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 |

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