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.

Author
Bo Li
Date of publication
2014-08-09 00:00:40
Maintainer
Bo Li <libo@umich.edu>
License
GPL (>= 2)
Version
1.1
URLs

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
CHAT/NAMESPACE
CHAT/data
CHAT/data/A0SD.LRR.rda
CHAT/data/A0SD.BAF.rda
CHAT/data/prior.rda
CHAT/data/datalist
CHAT/data/mcmc.rda
CHAT/R
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/MD5
CHAT/DESCRIPTION
CHAT/man
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