ELViS: an R package for estimating copy number levels of viral genomic segments at base-resolution.

Abstract

Tumor viruses account for ∼10% of cancer diagnoses. Virally induced tumorigenesis is understood as direct signaling through oncogenes such as E6 and E7 genes in the case of human papillomavirus. Furthermore, pathogen characteristics such as viral oncogene dose may impact the disease course. To our knowledge, no tool has been proposed to assess the intra-viral copy number alterations that define the gene dose of viral oncogenes and associated suppressive pathways native to the pathogen's normal life cycle. We propose an R package, "ELViS," that analyzes viral copy number changes from DNA sequencing of whole viral genomes. The method adjusts for viral load with 2D transformation and segmentation to offer the relative viral gene doses. The ELViS R package is available from https://bioconductor.org/packages/ELViS. This article used controlled access data from dbGaP (phs001713.v1.p1).