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 |
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