GCcontent


GC content was calculated for hg19 human genome at each 1Mb interval. SomatiCA uses this file to correct GC bias.


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

GCcontent function

A data frame with 2897 rows on the following 4 variables.
  <dl>
    <dt><code>chr</code></dt><dd>A character vector.</dd> <dt><code>interval1</code></dt><dd>A numeric vector.</dd> <dt><code>interval2</code></dt><dd>A numeric vector.</dd> <dt><code>GC</code></dt><dd>A numeric vector. GC content.</dd> </dl> 

Format

Assembly human genome (hg19,
GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)) was downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/.

GCcontent: GC content for hg19 human genome at each 1Mb interval.

Description

Usage

Arguments

Format

Source