In ojcharles/hsvdrg: Herpes Simplex Virus 1 and 2 Drug Resistance Genotyping

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hsvdrg

Overview

hsvdrg is a R package to enable antiviral drug resistance genotyping, with Herpes Simplex Virus 1 sequencing data. Accepted inputs are FASTA (whole genomes & fragments) which will be mapped to RefSeq NC_001806.2. NGS variant data assembled to NC_001806.2 is accepted in VCF >= ver4.0 & Varscan2 tab formats.

Database

All data extracted from https://academic.oup.com/jac/article/71/1/6/2363653 and contains the relationships between:

• Gene
• Mutation
• Drug susceptibility as "Resistant" or "Polymorphism"
• The method for Resistance Phenotyping
• Publication reference as in https://academic.oup.com/jac/article/71/1/6/2363653

Web service

A user-friendly Shiny Applications has been bundled with this package. The same application is available over the internet here http://cmv-resistance.ucl.ac.uk/hsvdrg/ where the terms of use are contained.

Installation

You can install the current version from GitHub with:

# install.packages("devtools")
devtools::install_github("ojcharles/hsvdrg")

Dependencies for FASTA file handling are MAFFT and SNP-Sites available preferably via conda. snp-sites >= 2.3 has been tested. ```{bash, eval=FALSE} conda config --add channels bioconda conda install snp-sites conda install mafft

## Usage

### vcf data

```r
library("hsvdrg")

## call resistant variants
my_sample = system.file("testdata", "F716L.vcf", package = "hsvdrg")

data = call_resistance(infile = my_sample, all_mutations = F)

data[ , c("change", "freq", "Aciclovir", "Pencyclovir", "Foscarnet")]


## call all variants
mutations_all = call_resistance(infile = my_sample, all_mutations = T)

#to view all mutations in resistance genes we can filter
mutations_res = mutations_all[mutations_all$GENEID %in% c("UL30"),]

head(mutations_res[,c(1,8,21,32:40)])


## call nonsynonymous variants
# are there any non-synonymous (DNA variants that result in a change of amino acid) variants in resistance genes
mutations_res_nonsyn = mutations_res[mutations_res$CONSEQUENCE == "nonsynonymous",]


# here the top 3 mutations are nonsynonymous, with no identified resistance effect.
head(mutations_res_nonsyn[,c(1,8,21,32:40)])

fasta sequences

# hsvdrg accepts sequence fragments or whole-genomes, one fasta sequence at a time.

# load example data
my_sequence = system.file("testdata", "F716L.fasta", package = "hsvdrg")

dat = call_resistance(infile = my_sequence, all_mutations = T)

head(dat)

other features

## view the full database
db = hsvdrg_data()
head(db$aa_change)


## run the shiny application
# runShinyHSV()

Getting help

If you encounter a clear bug, please file an issue with a minimal reproducible example on the GitHub Issues page. For questions and other discussions feel free to contact. Oscar Charles - maintainer

ojcharles/hsvdrg documentation built on Jan. 19, 2021, 2:02 p.m.