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CHAT (version 1.1)

Clonal Heterogeneity Analysis Tool

Description

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.

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Version

Install

install.packages('CHAT')

Monthly Downloads

20

Version

1.1

License

GPL (>= 2)

Maintainer

Last Published

August 8th, 2014

Functions in CHAT (1.1)

Segment-specific AGP inference by sample

CCF estimation main function

Merge adjacent break points

Find peaks on a curve

Find all the coordinates for canonical points

Fraction of loss-of-heterozygosity

getCanonicalLines

Regression lines on canonical points with same number of minor alleles

Distance from point to a line

B-allele frequencies of selected chromosomes for TCGA sample A1-A0SD.

plotIdentifiableZone

Plot Identifiable Zone on sAGP-SAF plot

Near canonical position

Copy number information of selected chromosomes for TCGA sample A1-A0SD.

Null distribution for estimated AGP.

Segment-specific AGP estimation main function

Perform DNA segmentation and calculate folded BAF and logR ratios.

Normal-Uniform mixture model fitting

Approximate BIC calculation

MCMC fitting of sAGP values

Clonal Heterogeneity Analysis Tool

Initialize parameters for sAGP estimation.

Compute the summation of distances

Prior parameters for MCMC

MCMC fitting for single sample

Initialize parameters for AGP estimation

getDiploidOrigin

Estimate diploid origin in higher ploidy samples

AGP inference by sample

Obtain germline heterozygous markers

MCMC parameters.

Compute mean of BAF

Inference of Origin Cluster

Find nearest distance from a data point to a canonical line

MergeBreakPointsByChr

Merge break points from two sets

Perform circular binary segmentation by chromosome

findRobustPeaks

Find well-separated peaks

Computes cosine value of the angle for two vectors.

Computes coordinates of a canonical point

Fraction of amplification or deletion in the genome

Normalize LRR values

Genomewide average ploidy

AGP estimation main function

CCF estimation by sample.

K-means clustering of data points

Perform binned DNA segmentation by chromosome