Usage

The R script cgMLSTcomparison.R aims at performing Principal Component Analysis (PCA) and Generalized Linear Model (GLM) from cgMLST outcomes described in the "Listeria-cgMLST-Additional-file-3.tsv" of the article entitled "In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes".

Dependencies

The R script DownsampledReads.R was prepared and tested with R version 3.6.3 and RStudio 1.3.1093.

• library(ggplot2)
• library(plyr)
• library(reshape2)
• library(tidyr)
• library(AER)
• library(spgs)
• library(usethis)
• library(devtools)
• library(ggbiplot)

Install R and Rstudio

1/ Install R (from configured sources)

sudo apt update
sudo apt install r-base
R --version

2/ Install RStudio (from dowloaded rstudio-1.3.1093-amd64.deb)

sudo apt install gdebi-core
sudo gdebi /home/Downloads/rstudio-1.3.1093-amd64.deb
rstudio --version

Update R

1/ Check the current R version

R --version

2/ Update and upgrade apt-get

sudo apt-get update
sudo apt-get upgrade

3/ Check the available latest R version

sudo apt-cache showpkg r-base

4/ Update the lastest R version

sudo apt-get install r-base

5/ Check the updated R version

R --version

Install devtools (Ubuntu 20.04)

sudo apt install libssl-dev

Follow step per step the R script with RStudio

rstudio cgMLSTcomparison.R

Illustration

Reference

Palma F., Mangone I., Janowicz A., Moura A., Chiaverini A., Torresi M., Garofolo G., Criscuolo A., Brisse S., Di Pasquale A., Cammà C. and Radomski N. In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes. 2022, BMC Genomics, 23(235): 1-24, https://doi.org/10.1186/s12864-022-08437-4

Acknowledgment

My former colleague Laurent Guillier with whom I learned a lot about R

Author

Nicolas Radomski