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.
You can install rhinotypeR from BioConductor using
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rhinotypeR")
library(rhinotypeR)
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")
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"))
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)