This is the development version of SARC; for the stable release version, see SARC.
Statistical Analysis of Regions with CNVsBioconductor version: Development (3.22)
Imports a cov/coverage file (normalised read coverages from BAM files) and a cnv file (list of CNVs - similiar to a BED file) from WES/ WGS CNV (copy number variation) detection pipelines and utilises several metrics to weigh the likelihood of a sample containing a detected CNV being a true CNV or a false positive. Highly useful for diagnostic testing to filter out false positives to provide clinicians with fewer variants to interpret. SARC uniquely only used cov and csv (similiar to BED file) files which are the common CNV pipeline calling filetypes, and can be used as to supplement the Interactive Genome Browser (IGV) to generate many figures automatedly, which can be especially helpful in large cohorts with 100s-1000s of patients.
Author: Krutik Patel [aut, cre] ORCID: 0000-0001-6806-8675
Maintainer: Krutik Patel <nkp68 at newcastle.ac.uk>
Citation (from within R, entercitation("SARC")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SARC")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SARC")Follow Installation instructions to use this package in your R session.
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