segwithratio


SomatiCA segmentation and somatic ratio estimation results for data(glio).


datasets

SomatiCA is a software suite that is capable of
identifying, characterizing, and quantifying somatic CNAs from
cancer genome sequencing. First, it uses read depths and lesser
allele frequencies (LAF) from mapped short sequence reads to
segment the genome and identify candidate CNAs. Second,
SomatiCA estimates the admixture rate from the relative
copy-number profile of tumor-normal pair by a Bayesian finite
mixture model. Third, SomatiCA quantifies absolute somatic
copy-number and subclonality for each genomic segment to guide
its characterization. Results from SomatiCA can be further
integrated with single nucleotide variations (SNVs) to get a
better understanding of the tumor evolution.

Mengjie Chen

SomatiCA

SomatiCA: identifying, characterizing, and quantifying somatic
copy number aberrations from cancer genome sequencing

segwithratio function

A data frame with 143 segments on the following 6 variables.
  <dl>
    <dt><code>chromosome</code></dt><dd>A character vector.</dd> <dt><code>start</code></dt><dd>An integer vector.</dd> <dt><code>end</code></dt><dd>An integer vector.</dd> <dt><code>medLAF</code></dt><dd>A numeric vector. Median LAF in tumor sample.</dd> <dt><code>medgermlineLAF</code></dt><dd>A numeric vector. Median LAF in control sample.</dd> <dt><code>ratio</code></dt><dd>A numeric vector. Estimated somatic ratio.</dd> </dl> 

segwithratio: Segments with somatic ratio.

Description

Usage

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