getDiploidOrigin


numeric matrix, as returned from getSegPurity()


para


In higher ploidy samples, the Origin Cluster estimated by getOrigin() usually represents the fraction of genome with balanced gains. This function estimates the position of the unchanged diploid genome on BAF-LRR plot.


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.

getDiploidOrigin: Estimate diploid origin in higher ploidy samples

Description

Usage

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Value