# Clonal Heterogeneity Analysis Tool

## Documentation for package ‘CHAT’ version 1.1

- DESCRIPTION file.

## Help Pages

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