Man pages for CHAT
Clonal Heterogeneity Analysis Tool

A0SD.BAFB-allele frequencies of selected chromosomes for TCGA sample...
A0SD.LRRCopy number information of selected chromosomes for TCGA...
ApproxBICApproximate BIC calculation
CHAT-packageClonal Heterogeneity Analysis Tool
DistDistance from point to a line
DPfitSamplesMCMC fitting of sAGP values
findRobustPeaksFind well-separated peaks
getAGPAGP estimation main function
getAmpDelFraction of amplification or deletion in the genome
getBAFmeanCompute mean of BAF
getCanonicalLinesRegression lines on canonical points with same number of...
getCCFCCF estimation main function
getCoordComputes coordinates of a canonical point
getCosineComputes cosine value of the angle for two vectors.
getDiploidOriginEstimate diploid origin in higher ploidy samples
getDistToPathFind nearest distance from a data point to a canonical line
getDPfitMCMC fitting for single sample
getGridFind all the coordinates for canonical points
getHetsObtain germline heterozygous markers
getKmeansK-means clustering of data points
getLOHFraction of loss-of-heterozygosity
getOriginInference of Origin Cluster
getParaInitialize parameters for AGP estimation
getPara.sAGPInitialize parameters for sAGP estimation.
getPeaksFind peaks on a curve
getPermutationNull distribution for estimated AGP.
getPloidyGenomewide average ploidy
getsAGPSegment-specific AGP estimation main function
getSampleAGPAGP inference by sample
getSampleCCFCCF estimation by sample.
getSegPerform DNA segmentation and calculate folded BAF and logR...
getSegChrPerform binned DNA segmentation by chromosome
getSegChr.CBSPerform circular binary segmentation by chromosome
getSegPuritySegment-specific AGP inference by sample
getSumDistCompute the summation of distances
getUnifiedMapMerge adjacent break points
is.nearCPNear canonical position
mcmcMCMC parameters.
MergeBreakPointsByChrMerge break points from two sets
NormalizeLRRNormalize LRR values
plotIdentifiableZonePlot Identifiable Zone on sAGP-SAF plot
priorPrior parameters for MCMC
SampleNMMNormal-Uniform mixture model fitting
CHAT documentation built on May 29, 2017, 10:32 p.m.