November 29th, 2018
NYC R/Bioconductor Meetup
Present by Sehyun Oh
Absolute copy number analysis requires simultaneous inference of purity, ploidy, and loss of heterozygosity. Commonly used algorithms rely on high quality genome-wide data with matched normal profiles, limiting their applicability in clinical settings. In this workshop, I will introduce a benchmark example of absolute copy number variation (CNV) analysis from tumor-only whole exome sequencing (WES) data, followed by a step-by-step tutorial on the analysis workflow. The workflow is based on PureCN, a R/Bioconductor package.
A tool developed for tumor-only diagnostic sequencing using hybrid-capture protocols. It provides copy number adjusted for purity and ploidy and can classify mutations by somatic status and clonality. It requires a pool of process-matched normals for coverage normalization and artifact filtering. (https://github.com/lima1/PureCN)
The major package we are using is PureCN.
To install this package, start R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("PureCN")
Some optional packages:
BiocManager::install("TCGAutils")
BiocManager::install("jsonlite")
BiocManager::install("curl")
BiocManager::install("downloader")
BiocManager::install("GenomicDataCommons")
BiocManager::install("magrittr")
BiocManager::install("rtracklayer")
http://rpubs.com/shbrief/meetup_1
http://rpubs.com/shbrief/meetup_2
Riester M, Singh A, Brannon A, Yu K, Campbell C, Chiang D and Morrissey M (2016). “PureCN: Copy number calling and SNV classification using targeted short read sequencing.” Source Code for Biology and Medicine, 11, pp. 13. doi: 10.1186/s13029-016-0060-z.