CHAT: Clonal Heterogeneity Analysis Tool

CHAT is a collection of tools developed for tumor subclonality analysis using high density DNA SNP array data and sequencing data. The pipeline consists of four major compartments: 1) tumor aneuploid genome proportion (AGP) calculation and ploidy estimation. 2) segment-specific AGP calculation and absolute copy number estimation for somatic CNAs. 3) cancer cell fraction correction for somatic SNVs in clonal or subclonal sCNA regions. 4) number of subclones estimation using Dirichlet process prior followed by MCMC approach.

AuthorBo Li
Date of publication2014-08-09 00:00:40
MaintainerBo Li <>
LicenseGPL (>= 2)

View on CRAN

Man pages

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

Files in this package

CHAT/R/getOrigin.R CHAT/R/getUnifiedMap.R CHAT/R/MergeBreakPointsByChr.R CHAT/R/getDistToPath.R CHAT/R/getSampleAGP.R CHAT/R/findRobustPeaks.R CHAT/R/plotBAFLRR.R CHAT/R/getBAFmean.R CHAT/R/getCanonicalLines.R CHAT/R/getDPfit.R CHAT/R/getPloidy.R CHAT/R/Dist.R CHAT/R/getPermutation.R CHAT/R/getHets.R CHAT/R/getDiploidOrigin.R CHAT/R/getCoord.R CHAT/R/getSeg.R CHAT/R/getAmpDel.R CHAT/R/getSegChr.R CHAT/R/getLOH.R CHAT/R/getGrid.R CHAT/R/getSampleCCF.R CHAT/R/getAGP.R CHAT/R/is.nearCP.R CHAT/R/getSumDist.R CHAT/R/ApproxBIC.R CHAT/R/getKmeans.R CHAT/R/getSegPurity.R CHAT/R/getCosine.R CHAT/R/getsAGP.R CHAT/R/getCCF.R CHAT/R/SampleNMM.R CHAT/R/plotIdentifiableZone.R CHAT/R/DPfitSamples.R CHAT/R/getPeaks.R CHAT/R/getPara.sAGP.R CHAT/R/getSegChr.CBS.R CHAT/R/getPara.R CHAT/R/NormalizeLRR.R
CHAT/man/findRobustPeaks.Rd CHAT/man/getOrigin.Rd CHAT/man/getsAGP.Rd CHAT/man/DPfitSamples.Rd CHAT/man/getSegChr.Rd CHAT/man/getCanonicalLines.Rd CHAT/man/getPara.sAGP.Rd CHAT/man/getDPfit.Rd CHAT/man/getPermutation.Rd CHAT/man/getHets.Rd CHAT/man/getDiploidOrigin.Rd CHAT/man/A0SD.BAF.Rd CHAT/man/getSumDist.Rd CHAT/man/SampleNMM.Rd CHAT/man/getAmpDel.Rd CHAT/man/ApproxBIC.Rd CHAT/man/getSeg.Rd CHAT/man/plotIdentifiableZone.Rd CHAT/man/getLOH.Rd CHAT/man/getSampleCCF.Rd CHAT/man/plotBAFLRR.Rd CHAT/man/getCosine.Rd CHAT/man/getCCF.Rd CHAT/man/getDistToPath.Rd CHAT/man/getPara.Rd CHAT/man/getSegPurity.Rd CHAT/man/getCoord.Rd CHAT/man/getKmeans.Rd CHAT/man/getSegChr.CBS.Rd CHAT/man/getPeaks.Rd CHAT/man/Dist.Rd CHAT/man/getSampleAGP.Rd CHAT/man/A0SD.LRR.Rd CHAT/man/CHAT-package.Rd CHAT/man/prior.Rd CHAT/man/MergeBreakPointsByChr.Rd CHAT/man/getUnifiedMap.Rd CHAT/man/getPloidy.Rd CHAT/man/getGrid.Rd CHAT/man/getAGP.Rd CHAT/man/NormalizeLRR.Rd CHAT/man/is.nearCP.Rd CHAT/man/getBAFmean.Rd CHAT/man/mcmc.Rd

Questions? Problems? Suggestions? or email at

All documentation is copyright its authors; we didn't write any of that.