Background

The rhinotypeR package is designed to simplify the genotyping of rhinoviruses using the VP4/2 genomic region. Having worked on rhinoviruses for a few years, I noticed that assigning genotypes after sequencing was particularly laborious, and needed several manual interventions. We, therefore, developed this package to address this challenge by streamlining the process by enabling a user to download prototype sequences, calculate genetic pairwise distances, and compare the distances to prototype strains for genotype assignment. It also provides visualization options such as frequency plots and simple phylogenetic trees.

Usage

Installing the package

You can install rhinotypeR from BioConductor using

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rhinotypeR")

Loading the package

library(rhinotypeR)

Example Workflow

  1. Download prototype sequences:

The getPrototypeSeqs function downloads the prototype sequences required for genotyping. These should the be combined with the newly generated sequences, aligned using a suitable software, and imported into R. For example, to download to the Desktop directory, one can run:

getPrototypeSeqs("~/Desktop")
  1. Read sequences:

Use the Biostrings package to read FASTA files containing sequence data. This extracts the sequence data and headers information and should be stored into an object for downstream analysis.

sequences <- Biostrings::readDNAStringSet(system.file("extdata", "input_aln.fasta", package="rhinotypeR"))
  1. Visualize SNPs:

The SNPeek function visualizes single nucleotide polymorphisms (SNPs) in the sequences, with a select sequence acting as the reference. To specify the reference sequences, move it to the bottom of the alignment before importing into R. Substitutions are color-coded by the nucleotide i.e.,

A = green

T = red

C = blue

G = yellow

SNPeek(sequences)