In quick2063706271/Cov2Comparator: Analyzing SARS covid-2 genome across different geographic regions

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
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Cov2Comparator

Description

The goal of Cov2Comparator is to analyze SARS covid-2 genome across different geographic regions including performing multiple sequence alignments and phylogenetic tree. Unlike other packages, this package allows easy retrival of genome data by inputting region. It can also perform multiple sequence alignments and phylogenetic tree. Comprehensible plots can be presented in both ultiple sequence alignments and phylogenetic tree.

This package is built on macOS 12.0.1. R version 4.0.5

Installation

You can install the development version of Cov2Comparator from GitHub with:

require("devtools")
devtools::install_github("quick2063706271/Cov2Comparator", build_vignettes = TRUE)
library("Cov2Comparator")

To run the shinyApp:

runCov2Comparator()

Overview

ls("package:Cov2Comparator")
data(package = "Cov2Comparator") 

Vignettes

browseVignettes("Cov2Comparator")

An overview of the package is illustrated below.

.
├── Cov2Comparator.Rproj
├── DESCRIPTION
├── LICENSE
├── LICENSE.md
├── NAMESPACE
├── R
│   ├── phylogeneticTree.R
│   ├── readData.R
│   ├── sysdata.rda
│   └── sequenceComparison.R
├── README.Rmd
├── README.md
├── data
│   │
│   └── simpleAlign.rda
├── inst
│   └── extdata
│       ├── MN985325.1.fasta
│       ├── MT066156.1.fasta
│       ├── MW309440.1.fasta
│       ├── NC_045512.2.fasta
│       ├── nameToCountry.txt
│       └── overviewCov2.png
├── man
│   ├── createTree.Rd
│   ├── figures
│   │   └── README-pressure-1.png
│   ├── getSequenceByRegion.Rd
│   ├── getSequencesByRegions.Rd
│   ├── multipleSeqAlign.Rd
│   ├── plotAlignment.Rd
│   ├── plotTree.Rd
│   └── readGenome.Rd
├── tests
│   ├── testthat
│   │   ├── Rplots.pdf
│   │   ├── _snaps
│   │   ├── test-createTree.R
│   │   ├── test-getSequenceByRegion.R
│   │   ├── test-getSequencesByRegions.R
│   │   ├── test-multipleSeqAlign.R
│   │   ├── test-plotAlignment.R
│   │   ├── test-plotTree.R
│   │   └── test-readGenome.R
│   └── testthat.R
└── vignettes
    ├── Cov2Comparator.R
    ├── Cov2Comparator.Rmd
    └── Cov2Comparator.html

Contributions

The author of this package is Kuai Yu. readGenome, getSequenceByRegion, getSequencesByRegions, plotAlignment functions make use of Biostrings package for converting fasta files and alignment to format DNAStringSet. getSequenceByRegion function also makes use of ape package to download sequence from Genbank online. multipleSeqAlign function uses msa package to perform multiple sequence alignment. plotAlignment package function also uses pheatmap package to plot the result. createTree function uses msa package to convert data type, and seqinr to convert alignment to distance matrix. Then ape package is used to create the tree. The plotTree function makes use of the graphic R package.

Reference

R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

Charif, D. and Lobry, J.R. (2007). SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Structural approaches to sequence evolution: Molecules, networks, populations, series Biological and Medical Physics, Biomedical Engineering, 207-232. Springer Verlag, New York.

Ulrich Bodenhofer, Enrico Bonatesta, Christoph Horejs-Kainrath, & Sepp Hochreiter (2015). msa: an R package for multiple sequence alignment. Bioinformatics, 31(24), 3997–3999.

Paradis E. & Schliep K. (2019). ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526-528.

Raivo Kolde (2019). pheatmap: Pretty Heatmaps. R package version 1.0.12. https://CRAN.R-project.org/package=pheatmap

BioRender. (2020). Image created by Silva, A. Retrieved November 16, 2021, from https://app.biorender.com/

Dean Attali and Tristan Edwards (2020). shinyalert: Easily Create Pretty Popup Messages (Modals) in 'Shiny'. R package version 2.0.0. https://CRAN.R-project.org/package=shinyalert

Fanny Meyer and Victor Perrier (2020). shinybusy: Busy Indicator for 'Shiny' Applications. R package version 0.2.2. https://CRAN.R-project.org/package=shinybusy

Acknowledgemments

This package was developed as part of an assessment for 2021 BCB410H: Applied Bioinformatics, University of Toronto, Toronto, CANADA.

quick2063706271/Cov2Comparator documentation built on Dec. 22, 2021, 10:59 a.m.